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(-)
Title: Easily Load and Install the 'EconDataverse'
Description: The 'EconDataverse' is a universe of open-source packages to work
seamlessly with economic data. This package is designed to make it easy to
install and load multiple 'EconDataverse' packages in a single step. Learn
more about the 'EconDataverse' at <https://www.econdataverse.org>.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between econdataverse versions 0.1.0 dated 2025-09-10 and 0.1.1 dated 2025-11-28
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NEWS.md |only R/attach.R | 2 ++ R/econdataverse-package.R | 2 ++ README.md | 23 +++++++++++++++++------ tests/testthat/_snaps/attach.md | 9 +++++---- 7 files changed, 38 insertions(+), 21 deletions(-)
Title: Turn Clean Data into Messy Data
Description: Take real or simulated data and salt it with errors commonly
found in the wild, such as pseudo-OCR errors, Unicode problems, numeric
fields with nonsensical punctuation, bad dates, etc.
Author: Matthew Lincoln [aut, cre]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between salty versions 0.1.1 dated 2024-08-31 and 0.1.2 dated 2025-11-28
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/salt_replace.R | 2 +- README.md | 20 ++++++++++---------- 5 files changed, 25 insertions(+), 20 deletions(-)
Title: Data Validation and Organization of Metadata for Local and
Remote Tables
Description: Validate data in data frames, 'tibble' objects, 'Spark'
'DataFrames', and database tables. Validation pipelines can be made using
easily-readable, consecutive validation steps. Upon execution of the
validation plan, several reporting options are available. User-defined
thresholds for failure rates allow for the determination of appropriate
reporting actions. Many other workflows are available including an
information management workflow, where the aim is to record, collect, and
generate useful information on data tables.
Author: Richard Iannone [aut, cre] ,
Mauricio Vargas [aut] ,
June Choe [aut] ,
Olivier Roy [ctb]
Maintainer: Richard Iannone <rich@posit.co>
Diff between pointblank versions 0.12.2 dated 2024-10-22 and 0.12.3 dated 2025-11-28
pointblank-0.12.2/pointblank/tests/testthat/test-action_levels.R |only pointblank-0.12.2/pointblank/tests/testthat/test-align_multiagent.R |only pointblank-0.12.2/pointblank/tests/testthat/test-create_informant.R |only pointblank-0.12.2/pointblank/tests/testthat/test-create_multiagent.R |only pointblank-0.12.2/pointblank/tests/testthat/test-label_glue.R |only pointblank-0.12.2/pointblank/tests/testthat/test-schema.R |only pointblank-0.12.2/pointblank/tests/testthat/test-snip_fns.R |only pointblank-0.12.2/pointblank/tests/testthat/test-stop_if_not.R |only pointblank-0.12.2/pointblank/tests/testthat/test-tidyselect-yaml_columns.R |only pointblank-0.12.3/pointblank/DESCRIPTION | 33 pointblank-0.12.3/pointblank/LICENSE | 2 pointblank-0.12.3/pointblank/MD5 | 372 +- pointblank-0.12.3/pointblank/NEWS.md | 40 pointblank-0.12.3/pointblank/R/action_levels.R | 230 - pointblank-0.12.3/pointblank/R/all_passed.R | 92 pointblank-0.12.3/pointblank/R/col_count_match.R | 194 - pointblank-0.12.3/pointblank/R/col_exists.R | 186 - pointblank-0.12.3/pointblank/R/col_is_character.R | 196 - pointblank-0.12.3/pointblank/R/col_is_date.R | 196 - pointblank-0.12.3/pointblank/R/col_is_factor.R | 204 - pointblank-0.12.3/pointblank/R/col_is_integer.R | 204 - pointblank-0.12.3/pointblank/R/col_is_logical.R | 198 - pointblank-0.12.3/pointblank/R/col_is_numeric.R | 196 - pointblank-0.12.3/pointblank/R/col_is_posix.R | 198 - pointblank-0.12.3/pointblank/R/col_schema_match.R | 310 +- pointblank-0.12.3/pointblank/R/col_vals_between.R | 250 - pointblank-0.12.3/pointblank/R/col_vals_decreasing.R | 241 - pointblank-0.12.3/pointblank/R/col_vals_equal.R | 237 - pointblank-0.12.3/pointblank/R/col_vals_expr.R | 257 + pointblank-0.12.3/pointblank/R/col_vals_gt.R | 299 +- pointblank-0.12.3/pointblank/R/col_vals_gte.R | 231 - pointblank-0.12.3/pointblank/R/col_vals_in_set.R | 229 - pointblank-0.12.3/pointblank/R/col_vals_increasing.R | 239 - pointblank-0.12.3/pointblank/R/col_vals_lt.R | 231 - pointblank-0.12.3/pointblank/R/col_vals_lte.R | 235 - pointblank-0.12.3/pointblank/R/col_vals_make_set.R | 229 - pointblank-0.12.3/pointblank/R/col_vals_make_subset.R | 231 - pointblank-0.12.3/pointblank/R/col_vals_not_between.R | 260 - pointblank-0.12.3/pointblank/R/col_vals_not_equal.R | 233 - pointblank-0.12.3/pointblank/R/col_vals_not_in_set.R | 225 - pointblank-0.12.3/pointblank/R/col_vals_not_null.R | 219 - pointblank-0.12.3/pointblank/R/col_vals_null.R | 219 - pointblank-0.12.3/pointblank/R/col_vals_regex.R | 229 - pointblank-0.12.3/pointblank/R/col_vals_within_spec.R | 287 -- pointblank-0.12.3/pointblank/R/column_roles.R | 448 +-- pointblank-0.12.3/pointblank/R/conjointly.R | 216 - pointblank-0.12.3/pointblank/R/create_agent.R | 267 - pointblank-0.12.3/pointblank/R/create_informant.R | 196 - pointblank-0.12.3/pointblank/R/create_multiagent.R | 100 pointblank-0.12.3/pointblank/R/datasets.R | 42 pointblank-0.12.3/pointblank/R/draft_validation.R | 334 +- 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pointblank-0.12.3/pointblank/tests/testthat/test-tidyselect_integration.R | 150 - pointblank-0.12.3/pointblank/tests/testthat/test-x_list.R | 307 +- 193 files changed, 12560 insertions(+), 12358 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
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>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.1.1 dated 2025-10-09 and 5.0.2 dated 2025-11-28
nlmixr2est-4.1.1/nlmixr2est/tests/testthat/datos_pac.qs |only nlmixr2est-4.1.1/nlmixr2est/tests/testthat/out.focei.prop.qs |only nlmixr2est-4.1.1/nlmixr2est/tests/testthat/test-cwres-3.0.3.qs |only nlmixr2est-4.1.1/nlmixr2est/tests/testthat/test-resume-bobyqa.qs |only nlmixr2est-4.1.1/nlmixr2est/tests/testthat/test-saem-theo_sd.qs |only nlmixr2est-5.0.2/nlmixr2est/DESCRIPTION | 12 nlmixr2est-5.0.2/nlmixr2est/MD5 | 85 +-- nlmixr2est-5.0.2/nlmixr2est/NEWS.md | 7 nlmixr2est-5.0.2/nlmixr2est/R/bobyqa.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/compat.R | 11 nlmixr2est-5.0.2/nlmixr2est/R/focei.R | 8 nlmixr2est-5.0.2/nlmixr2est/R/foceiControl.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/lbfgsb3c.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/n1qn1.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/newuoa.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nlm.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nlme.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nlminb.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nls.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/nmObjGet.R | 17 nlmixr2est-5.0.2/nlmixr2est/R/optim.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/saemControl.R | 2 nlmixr2est-5.0.2/nlmixr2est/R/uobyqa.R | 2 nlmixr2est-5.0.2/nlmixr2est/man/bobyqaControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/foceiControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/lbfgsb3cControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/n1qn1Control.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/newuoaControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/nlmControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/nlminbControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/nlmixr2NlmeControl.Rd | 4 nlmixr2est-5.0.2/nlmixr2est/man/nlsControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/optimControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/saemControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/man/uobyqaControl.Rd | 2 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-addCwres.R | 4 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-focei-cens.R | 249 +++++----- nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-focei-wang2007.R | 2 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-posthoc.R | 3 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-restart.R | 5 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-restart.qs2 |only nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-resume-bobyqa.R | 2 nlmixr2est-5.0.2/nlmixr2est/tests/testthat/test-saem-theo_sd.R | 6 nlmixr2est-5.0.2/nlmixr2est/tests/testthatdatos_pac.qs2 |only nlmixr2est-5.0.2/nlmixr2est/tests/testthatout.focei.prop.qs2 |only nlmixr2est-5.0.2/nlmixr2est/tests/testthattest-cwres-3.0.3.qs2 |only nlmixr2est-5.0.2/nlmixr2est/tests/testthattest-resume-bobyqa.qs2 |only nlmixr2est-5.0.2/nlmixr2est/tests/testthattest-saem-theo_sd.qs2 |only 49 files changed, 251 insertions(+), 212 deletions(-)
Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group
Structure
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Author: Yazdan Asgari [aut, cre],
Taban Baghfalaki [aut],
Benoit Liquet [aut],
Pierre-Emmanuel Sugier [aut],
Mohammed Sedki [aut],
Therese Truong [aut]
Maintainer: Yazdan Asgari <yazdan.asgari@inserm.fr>
Diff between GCPBayes versions 4.2.0 dated 2024-03-14 and 4.3.0 dated 2025-11-28
DESCRIPTION | 10 ++++----- MD5 | 36 +++++++++++++++++------------------ NAMESPACE | 14 ++++--------- NEWS.md | 7 ++++++ R/CS.R | 14 ++++++++++--- R/DS.R | 12 +++++++++-- R/GCPBayes.R | 2 + R/HS.R | 7 ++++-- R/MCMCplot.R | 2 + inst/examplesummaryHS.R | 2 - man/CS.Rd | 4 +-- man/DS.Rd | 3 +- man/GCPBayes.Rd | 12 +++++++++-- man/HS.Rd | 6 ++--- man/Simulated_individual_survival.Rd | 1 man/summaryCS.Rd | 4 +-- man/summaryDS.Rd | 4 +-- man/summaryHS.Rd | 10 ++++----- src/Makevars | 3 ++ 19 files changed, 95 insertions(+), 58 deletions(-)
Title: Autodiff for Influence Function Based Estimates
Description: Implements an S7 class for estimates based on influence functions,
with forward mode automatic differentiation defined for standard arithmetic
operations.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between ife versions 0.2.0 dated 2025-08-18 and 0.2.1 dated 2025-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/influence_func_estimand.R | 11 +++++------ 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Submitter and Monitor of the 'LSF Cluster'
Description: It submits R code/R scripts/shell commands to 'LSF cluster'
(<https://en.wikipedia.org/wiki/Platform_LSF>, the 'bsub' system) without
leaving R. There is also an interactive 'shiny' application for monitoring job status.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between bsub versions 1.1.0 dated 2021-07-01 and 2.0.6 dated 2025-11-28
bsub-1.1.0/bsub/R/clear.R |only bsub-1.1.0/bsub/inst/app/format.js |only bsub-1.1.0/bsub/man/bjobs_barplot.Rd |only bsub-1.1.0/bsub/man/bjobs_done.Rd |only bsub-1.1.0/bsub/man/bjobs_exit.Rd |only bsub-1.1.0/bsub/man/bjobs_pending.Rd |only bsub-1.1.0/bsub/man/bjobs_running.Rd |only bsub-1.1.0/bsub/man/bjobs_timeline.Rd |only bsub-1.1.0/bsub/man/brecent.Rd |only bsub-1.1.0/bsub/man/bsub_chunk.Rd |only bsub-1.1.0/bsub/man/bsub_cmd.Rd |only bsub-1.1.0/bsub/man/bsub_script.Rd |only bsub-1.1.0/bsub/man/check_dump_files.Rd |only bsub-1.1.0/bsub/man/clear_temp_dir.Rd |only bsub-1.1.0/bsub/man/get_dependency.Rd |only bsub-1.1.0/bsub/man/is_job_finished.Rd |only bsub-1.1.0/bsub/man/job_status_by_id.Rd |only bsub-1.1.0/bsub/man/job_status_by_name.Rd |only bsub-1.1.0/bsub/man/plot_dependency.Rd |only bsub-1.1.0/bsub/man/print.bconf.Rd |only bsub-1.1.0/bsub/man/ssh_connect.Rd |only bsub-1.1.0/bsub/man/ssh_disconnect.Rd |only bsub-1.1.0/bsub/man/wait_jobs.Rd |only bsub-2.0.6/bsub/DESCRIPTION | 27 bsub-2.0.6/bsub/LICENSE | 3 bsub-2.0.6/bsub/MD5 | 101 +- bsub-2.0.6/bsub/NAMESPACE | 108 +-- bsub-2.0.6/bsub/NEWS | 39 + bsub-2.0.6/bsub/R/bjobs.R |only bsub-2.0.6/bsub/R/bsub.R | 602 +++++++++-------- bsub-2.0.6/bsub/R/clean.R |only bsub-2.0.6/bsub/R/config.R | 63 + bsub-2.0.6/bsub/R/dependency.R | 241 +++---- bsub-2.0.6/bsub/R/format.R | 81 ++ bsub-2.0.6/bsub/R/global.R | 226 +++--- bsub-2.0.6/bsub/R/job_log.R |only bsub-2.0.6/bsub/R/monitor.R | 926 ++------------------------- bsub-2.0.6/bsub/R/pipeline.R |only bsub-2.0.6/bsub/R/rerun.R |only bsub-2.0.6/bsub/R/retrieve.R |only bsub-2.0.6/bsub/R/run_cmd.R |only bsub-2.0.6/bsub/R/ssh.R | 77 -- bsub-2.0.6/bsub/R/status.R |only bsub-2.0.6/bsub/R/utils.R |only bsub-2.0.6/bsub/R/zzz.R | 40 - bsub-2.0.6/bsub/build/vignette.rds |binary bsub-2.0.6/bsub/inst/app/app.R | 440 ++++++++---- bsub-2.0.6/bsub/inst/app/app.js |only bsub-2.0.6/bsub/inst/app/style.css |only bsub-2.0.6/bsub/inst/bsub_test/bsub_test.R | 3 bsub-2.0.6/bsub/inst/doc/bsub.Rmd | 6 bsub-2.0.6/bsub/inst/doc/bsub.html | 223 ++++++ bsub-2.0.6/bsub/man/bconf.Rd | 30 bsub-2.0.6/bsub/man/bjobs.Rd | 104 ++- bsub-2.0.6/bsub/man/bjobs_reset_timestamp.Rd |only bsub-2.0.6/bsub/man/bkill.Rd | 21 bsub-2.0.6/bsub/man/bsub.Rd |only bsub-2.0.6/bsub/man/bsub_opt.Rd | 103 +-- bsub-2.0.6/bsub/man/config_bsub.Rd |only bsub-2.0.6/bsub/man/dependency.Rd |only bsub-2.0.6/bsub/man/formatFileSize.Rd |only bsub-2.0.6/bsub/man/job_log.Rd | 20 bsub-2.0.6/bsub/man/job_status.Rd |only bsub-2.0.6/bsub/man/list_dump_files.Rd |only bsub-2.0.6/bsub/man/list_temp_files.Rd |only bsub-2.0.6/bsub/man/monitor.Rd | 18 bsub-2.0.6/bsub/man/print.bjobs.Rd | 22 bsub-2.0.6/bsub/man/random_job.Rd | 28 bsub-2.0.6/bsub/man/rerun.Rd |only bsub-2.0.6/bsub/man/retrieve_var.Rd | 30 bsub-2.0.6/bsub/man/run_cmd.Rd | 23 bsub-2.0.6/bsub/man/ssh.Rd |only bsub-2.0.6/bsub/man/visualize.Rd |only bsub-2.0.6/bsub/vignettes/bsub.Rmd | 6 74 files changed, 1735 insertions(+), 1876 deletions(-)
Title: Text Analysis with Rules and Dictionaries for Inferring
Sentiment
Description: Measure text's sentiment with dictionaries and simple rules covering
negations and modifiers. User-supplied dictionaries are supported, including
Unicode emojis and multi-word tokens, so this package can also be used to
study constructs beyond sentiment.
Author: Christopher Belanger [aut, cre, cph]
Maintainer: Christopher Belanger <christopher.a.belanger@gmail.com>
Diff between tardis versions 0.1.4 dated 2022-11-18 and 0.1.5 dated 2025-11-28
DESCRIPTION | 13 - MD5 | 10 - NEWS.md | 4 build/vignette.rds |binary inst/doc/tardis.R | 2 inst/doc/tardis.html | 403 +++++++++++++++++++-------------------------------- 6 files changed, 171 insertions(+), 261 deletions(-)
Title: Process Data from Wearable Light Loggers and Optical Radiation
Dosimeters
Description: Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Author: Johannes Zauner [aut, cre] ,
Manuel Spitschan [aut] ,
Steffen Hartmeyer [aut] ,
European Partnership on Metrology [fnd]
has received funding from the European Partnership on Metrology,
co-financed by the European Union's Horizon Europe Research and
[...truncated...]
Maintainer: Johannes Zauner <johannes.zauner@tum.de>
Diff between LightLogR versions 0.9.2 dated 2025-06-10 and 0.10.0 dated 2025-11-28
LightLogR-0.10.0/LightLogR/DESCRIPTION | 48 +-- LightLogR-0.10.0/LightLogR/MD5 | 154 +++++----- LightLogR-0.10.0/LightLogR/NAMESPACE | 10 LightLogR-0.10.0/LightLogR/NEWS.md | 92 +++++ LightLogR-0.10.0/LightLogR/R/Brown.R | 6 LightLogR-0.10.0/LightLogR/R/Circular2Time.R |only LightLogR-0.10.0/LightLogR/R/Datetime2Time.R | 41 ++ LightLogR-0.10.0/LightLogR/R/LightLogR-package.R | 1 LightLogR-0.10.0/LightLogR/R/aaa.r | 5 LightLogR-0.10.0/LightLogR/R/add_Date_col.R | 24 + LightLogR-0.10.0/LightLogR/R/add_states.R |only LightLogR-0.10.0/LightLogR/R/aggregate_Datetime.R | 15 LightLogR-0.10.0/LightLogR/R/coordinates.R |only LightLogR-0.10.0/LightLogR/R/extract_metric.R | 22 - LightLogR-0.10.0/LightLogR/R/extract_states.R | 150 --------- LightLogR-0.10.0/LightLogR/R/filter_Datetime.R | 29 + LightLogR-0.10.0/LightLogR/R/gg_day.r | 11 LightLogR-0.10.0/LightLogR/R/gg_days.R | 12 LightLogR-0.10.0/LightLogR/R/gg_gaps.R | 6 LightLogR-0.10.0/LightLogR/R/gg_heatmap.R | 13 LightLogR-0.10.0/LightLogR/R/gg_overview.R | 3 LightLogR-0.10.0/LightLogR/R/gg_state.R | 127 ++++++-- LightLogR-0.10.0/LightLogR/R/helper.R | 30 + LightLogR-0.10.0/LightLogR/R/import_LL.R | 55 ++- LightLogR-0.10.0/LightLogR/R/import_expressions.R | 135 ++++---- LightLogR-0.10.0/LightLogR/R/import_helper.r | 13 LightLogR-0.10.0/LightLogR/R/mean_daily.R | 7 LightLogR-0.10.0/LightLogR/R/normalise.R | 19 - LightLogR-0.10.0/LightLogR/R/photoperiod.R | 56 ++- LightLogR-0.10.0/LightLogR/R/remove_partial_data.R | 28 + LightLogR-0.10.0/LightLogR/R/sample_groups.R |only LightLogR-0.10.0/LightLogR/R/sc2interval.R | 12 LightLogR-0.10.0/LightLogR/R/sleepint2Brown.R | 55 ++- LightLogR-0.10.0/LightLogR/R/summarize_numeric.R | 6 LightLogR-0.10.0/LightLogR/R/summary_table.R |only LightLogR-0.10.0/LightLogR/R/supported_devices.R | 57 +++ LightLogR-0.10.0/LightLogR/README.md | 18 - LightLogR-0.10.0/LightLogR/inst/CITATION | 30 + LightLogR-0.10.0/LightLogR/man/Brown_check.Rd | 2 LightLogR-0.10.0/LightLogR/man/Circular2Time.Rd |only LightLogR-0.10.0/LightLogR/man/Datetime2Time.Rd | 6 LightLogR-0.10.0/LightLogR/man/LightLogR-package.Rd | 8 LightLogR-0.10.0/LightLogR/man/add_Date_col.Rd | 7 LightLogR-0.10.0/LightLogR/man/add_states.Rd | 29 + LightLogR-0.10.0/LightLogR/man/aggregate_Date.Rd | 7 LightLogR-0.10.0/LightLogR/man/aggregate_Datetime.Rd | 7 LightLogR-0.10.0/LightLogR/man/extract_metric.Rd | 2 LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-19-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-20-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-3-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-4-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-5-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-6-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/README-unnamed-chunk-7-1.png |binary LightLogR-0.10.0/LightLogR/man/figures/lifecycle-deprecated.svg |only LightLogR-0.10.0/LightLogR/man/figures/lifecycle-experimental.svg |only LightLogR-0.10.0/LightLogR/man/figures/lifecycle-stable.svg |only LightLogR-0.10.0/LightLogR/man/figures/lifecycle-superseded.svg |only LightLogR-0.10.0/LightLogR/man/filter_Datetime.Rd | 42 +- LightLogR-0.10.0/LightLogR/man/format_coordinates.Rd |only LightLogR-0.10.0/LightLogR/man/gg_day.Rd | 24 - 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Title: Generate Functions to Get or Set Global Options
Description: It provides more configurations on the option values such as validation
and filtering on the values, making options invisible or private.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GlobalOptions versions 0.1.2 dated 2020-06-10 and 0.1.3 dated 2025-11-28
GlobalOptions-0.1.2/GlobalOptions/man/Assign.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/Dot.DollarNames.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/Dot.v.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/Extract.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/ExtractExtract.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/ExtractExtractAssign.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/Subset.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/Subset.InternalOptionValue.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/dump_opt.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/print.GlobalOptionsFun.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/setGlobalOptions.Rd |only GlobalOptions-0.1.2/GlobalOptions/man/set_opt.Rd |only GlobalOptions-0.1.3/GlobalOptions/DESCRIPTION | 20 GlobalOptions-0.1.3/GlobalOptions/LICENSE | 3 GlobalOptions-0.1.3/GlobalOptions/MD5 | 36 GlobalOptions-0.1.3/GlobalOptions/NEWS | 6 GlobalOptions-0.1.3/GlobalOptions/build/vignette.rds |binary GlobalOptions-0.1.3/GlobalOptions/inst/doc/GlobalOptions.R | 2 GlobalOptions-0.1.3/GlobalOptions/inst/doc/GlobalOptions.html | 462 +++++----- GlobalOptions-0.1.3/GlobalOptions/man/Assign.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/Dot.DollarNames.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/Dot.v.rd |only GlobalOptions-0.1.3/GlobalOptions/man/Extract.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/ExtractExtract.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/ExtractExtractAssign.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/Subset.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/Subset.InternalOptionValue.rd |only GlobalOptions-0.1.3/GlobalOptions/man/dump_opt.rd |only GlobalOptions-0.1.3/GlobalOptions/man/print.GlobalOptionsFun.rd |only GlobalOptions-0.1.3/GlobalOptions/man/setGlobalOptions.rd |only GlobalOptions-0.1.3/GlobalOptions/man/set_opt.rd |only 31 files changed, 311 insertions(+), 218 deletions(-)
Title: Parsing Command-Line Arguments and Simple Variable Interpolation
Description: This is a command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptations for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 1.0.5 dated 2020-12-15 and 1.1.0 dated 2025-11-28
DESCRIPTION | 16 LICENSE | 2 MD5 | 36 + NAMESPACE | 1 NEWS | 14 R/0_global.R | 4 R/SingleOption-class.R | 32 - R/get_options.R | 58 ++ R/print.R | 81 +-- R/sub_commands.R |only build/vignette.rds |binary inst/doc/GetoptLong.R | 411 ++++++++++---------- inst/doc/GetoptLong.html | 717 ++++++++++++++++++++--------------- inst/doc/sub_commands.R |only inst/doc/sub_commands.Rmd |only inst/doc/sub_commands.html |only inst/doc/variable_interpolation.R | 44 +- inst/doc/variable_interpolation.html | 394 ++++++++----------- man/subCommands.Rd |only tests/testthat/test_GetoptLong.R | 36 + vignettes/GetoptLong.Rmd2 | 103 ++++- vignettes/sub_commands.Rmd |only 22 files changed, 1107 insertions(+), 842 deletions(-)
Title: Ensemble Learning Framework for Diagnostic and Prognostic
Modeling
Description: Provides a framework to build and evaluate diagnosis or
prognosis models using stacking, voting, and bagging ensemble
techniques with various base learners. The package also includes
tools for visualization and interpretation of models. The development
version of the package is available on 'GitHub' at
<https://github.com/xiaojie0519/E2E>. The methods
are based on the foundational work of Breiman (1996) <doi:10.1007/BF00058655>
on bagging and Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1>
on stacking.
Author: Shanjie Luan [aut, cre]
Maintainer: Shanjie Luan <Luan20050519@163.com>
Diff between E2E versions 0.1.0 dated 2025-09-04 and 0.1.1 dated 2025-11-28
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Title: Tools to Use and Explore the 'BioTIME' Database
Description: The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.
Author: Alban Sagouis [aut, cre] ,
Faye Moyes [aut] ,
Ines S. Martins [aut, rev] ,
Shane A. Blowes [ctb] ,
Viviana Brambilla [ctb] ,
Cher F. Y. Chow [ctb] ,
Ada Fontrodona-Eslava [ctb] ,
Laura Antao [ctb, rev] ,
Jonathan M. Chase [fnd] ,
Maria Dornelas [fnd, [...truncated...]
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
Diff between BioTIMEr versions 0.2.6 dated 2025-10-15 and 0.3.0 dated 2025-11-28
BioTIMEr-0.2.6/BioTIMEr/R/rarefyBioTIME.R |only BioTIMEr-0.2.6/BioTIMEr/inst/doc/vignette1.R |only BioTIMEr-0.2.6/BioTIMEr/inst/doc/vignette1.Rmd |only BioTIMEr-0.2.6/BioTIMEr/inst/doc/vignette1.html |only BioTIMEr-0.2.6/BioTIMEr/man/BioTIME-plots.Rd |only BioTIMEr-0.2.6/BioTIMEr/man/rarefysamples.Rd |only BioTIMEr-0.2.6/BioTIMEr/tests/testthat/_snaps/runResampling.md |only BioTIMEr-0.2.6/BioTIMEr/tests/testthat/test-rarefysamples.R |only BioTIMEr-0.2.6/BioTIMEr/tests/testthat/test-runResampling.R |only BioTIMEr-0.2.6/BioTIMEr/vignettes/vignette1.Rmd |only BioTIMEr-0.3.0/BioTIMEr/DESCRIPTION | 29 BioTIMEr-0.3.0/BioTIMEr/MD5 | 127 BioTIMEr-0.3.0/BioTIMEr/NAMESPACE | 23 BioTIMEr-0.3.0/BioTIMEr/NEWS.md | 69 BioTIMEr-0.3.0/BioTIMEr/R/BioTIMEr-package.R | 19 BioTIMEr-0.3.0/BioTIMEr/R/gridBioTIME.R | 258 BioTIMEr-0.3.0/BioTIMEr/R/metricsBioTIME.R | 244 BioTIMEr-0.3.0/BioTIMEr/R/plotsBioTIME.R | 126 BioTIMEr-0.3.0/BioTIMEr/R/resamplingBioTIME.R |only BioTIMEr-0.3.0/BioTIMEr/R/slopesBioTIME.R | 498 BioTIMEr-0.3.0/BioTIMEr/README.md | 4 BioTIMEr-0.3.0/BioTIMEr/build/vignette.rds |binary BioTIMEr-0.3.0/BioTIMEr/data/BTsubset_data.RData |binary BioTIMEr-0.3.0/BioTIMEr/data/BTsubset_meta.RData |binary BioTIMEr-0.3.0/BioTIMEr/inst/doc/introduction.R |only BioTIMEr-0.3.0/BioTIMEr/inst/doc/introduction.html |only BioTIMEr-0.3.0/BioTIMEr/inst/doc/introduction.qmd |only BioTIMEr-0.3.0/BioTIMEr/man/BioTIMEr-package.Rd | 3 BioTIMEr-0.3.0/BioTIMEr/man/getAlpha.Rd | 17 BioTIMEr-0.3.0/BioTIMEr/man/getAlphaMetrics.Rd | 56 BioTIMEr-0.3.0/BioTIMEr/man/getBeta.Rd | 4 BioTIMEr-0.3.0/BioTIMEr/man/getBetaMetrics.Rd | 35 BioTIMEr-0.3.0/BioTIMEr/man/getLinearRegressions.Rd | 26 BioTIMEr-0.3.0/BioTIMEr/man/gridding.Rd | 25 BioTIMEr-0.3.0/BioTIMEr/man/gridding_internal.Rd |only BioTIMEr-0.3.0/BioTIMEr/man/plotSlopes.Rd |only BioTIMEr-0.3.0/BioTIMEr/man/resampling.Rd | 32 BioTIMEr-0.3.0/BioTIMEr/man/resampling_core.Rd |only BioTIMEr-0.3.0/BioTIMEr/man/themeBioTIME.Rd |only 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BioTIMEr-0.3.0/BioTIMEr/tests/testthat/_snaps/slopes.md | 219 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/_snaps/workflow_alpha.md |10454 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/_snaps/workflow_beta.md | 4394 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-gridding.R | 51 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-metrics.R | 70 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-plots.R | 101 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling_abundance.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling_abundance_biomass.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling_abundance_biomass_conservative.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling_biomass.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-resampling_core.R |only BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-slopes.R | 46 BioTIMEr-0.3.0/BioTIMEr/tests/testthat/test-workflow_alpha.R | 31 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Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv',
'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut] ,
Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Shelby Bearrows [ctb],
https://github.com/mandreyel/ [cph] ,
Jukka Jylaenki [cph] ,
Mikkel Joergensen [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between vroom versions 1.6.6 dated 2025-09-19 and 1.6.7 dated 2025-11-28
DESCRIPTION | 13 LICENSE | 2 MD5 | 228 ++-- NEWS.md | 10 R/altrep.R | 6 R/col_types.R | 240 +++- R/date.R | 11 R/example.R | 4 R/generator.R | 118 +- R/locale.R | 48 R/path.R | 305 +++--- R/problems.R | 2 R/utils.R | 17 R/vroom.R | 176 ++- R/vroom_fwf.R | 90 + R/vroom_lines.R | 51 - R/vroom_write.R | 150 ++ R/zzz.R | 2 README.md | 26 build/stage23.rdb |binary build/vignette.rds |binary inst/WORDLIST | 7 inst/bench/all_character-long/data.table-data.table.R | 2 inst/bench/all_character-long/input.R | 12 inst/bench/all_character-long/readr-dplyr.R | 5 inst/bench/all_character-long/vroom-base.R | 8 inst/bench/all_character-long/vroom-dplyr.R | 13 inst/bench/all_character-long/vroom_no_altrep-dplyr.R | 14 inst/bench/all_character-wide/data.table-data.table.R | 2 inst/bench/all_character-wide/input.R | 12 inst/bench/all_character-wide/readr-dplyr.R | 5 inst/bench/all_character-wide/vroom-base.R | 8 inst/bench/all_character-wide/vroom-dplyr.R | 13 inst/bench/all_character-wide/vroom_no_altrep-dplyr.R | 14 inst/bench/all_numeric-long/data.table-data.table.R | 2 inst/bench/all_numeric-long/readr-dplyr.R | 5 inst/bench/all_numeric-long/vroom-base.R | 8 inst/bench/all_numeric-long/vroom-dplyr.R | 13 inst/bench/all_numeric-long/vroom_no_altrep-base.R | 9 inst/bench/all_numeric-long/vroom_no_altrep-dplyr.R | 14 inst/bench/all_numeric-wide/data.table-data.table.R | 2 inst/bench/all_numeric-wide/readr-dplyr.R | 5 inst/bench/all_numeric-wide/vroom-base.R | 8 inst/bench/all_numeric-wide/vroom-dplyr.R | 13 inst/bench/all_numeric-wide/vroom_no_altrep-base.R | 9 inst/bench/all_numeric-wide/vroom_no_altrep-dplyr.R | 14 inst/bench/fwf/read.delim-base.R | 2 inst/bench/fwf/readr-dplyr.R | 5 inst/bench/fwf/vroom-base.R | 2 inst/bench/fwf/vroom-dplyr.R | 5 inst/bench/fwf/vroom_no_altrep-dplyr.R | 5 inst/bench/run-bench-fwf.R | 14 inst/bench/run-bench.R | 5 inst/bench/session_info.R | 6 inst/bench/summarise-benchmarks.R | 56 - inst/bench/taxi/data.table-data.table.R | 2 inst/bench/taxi/read.delim-base.R | 8 inst/bench/taxi/readr-dplyr.R | 13 inst/bench/taxi/vroom-base.R | 9 inst/bench/taxi/vroom-dplyr.R | 14 inst/bench/taxi/vroom_no_altrep-dplyr.R | 15 inst/bench/taxi_multiple/data.table-data.table.R | 14 inst/bench/taxi_multiple/readr-dplyr.R | 18 inst/bench/taxi_multiple/vroom-base.R | 11 inst/bench/taxi_multiple/vroom-dplyr.R | 16 inst/bench/taxi_multiple/vroom_no_altrep-dplyr.R | 16 inst/bench/taxi_writing/base-uncompressed.R | 8 inst/bench/taxi_writing/vroom-multithreaded_gzip.R | 6 inst/bench/taxi_writing/vroom-zstandard.R | 6 inst/doc/benchmarks.R | 54 - inst/doc/benchmarks.Rmd | 58 - inst/doc/vroom.R | 4 inst/doc/vroom.Rmd | 6 inst/doc/vroom.html | 18 man/figures/lifecycle-superseded.svg | 2 man/vroom-package.Rd | 2 src/altrep.cc | 37 src/altrep.h | 6 src/columns.h | 3 src/index.h | 9 src/vroom_big_int.h | 2 src/vroom_chr.cc | 2 src/vroom_chr.h | 2 src/vroom_date.h | 2 src/vroom_dbl.h | 2 src/vroom_dttm.h | 2 src/vroom_errors.h | 8 src/vroom_fct.h | 2 src/vroom_int.h | 2 src/vroom_num.h | 2 src/vroom_rle.h | 4 src/vroom_time.h | 2 src/vroom_vec.h | 2 tests/spelling.R | 10 tests/testthat/helper.R | 108 +- tests/testthat/test-big-int.R | 86 + tests/testthat/test-chr.R | 16 tests/testthat/test-col_types.R | 11 tests/testthat/test-connection.R | 21 tests/testthat/test-datetime.R | 309 +++++- tests/testthat/test-dbl.R | 70 + tests/testthat/test-factor.R | 183 ++- tests/testthat/test-int.R | 34 tests/testthat/test-logical.R | 45 tests/testthat/test-multi-byte.R | 20 tests/testthat/test-multi-file.R | 141 +- tests/testthat/test-path.R | 19 tests/testthat/test-problems.R | 91 + tests/testthat/test-select.R | 160 ++- tests/testthat/test-vroom.R | 911 +++++++++++++----- tests/testthat/test-vroom_fwf.R | 269 ++++- tests/testthat/test-vroom_lines.R | 20 tests/testthat/test-vroom_write.R | 94 + vignettes/benchmarks.Rmd | 58 - vignettes/vroom.Rmd | 6 115 files changed, 3556 insertions(+), 1331 deletions(-)
Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574>,
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565> and
Laudanno et al. 2021. Syst. Biol. 70: 389–407,
<DOI:10.1093/sysbio/syaa048>.
Also contains functions to simulate the diversity-dependent
process.
Author: Rampal S. Etienne [aut, cre] ,
Bart Haegeman [aut] ,
Hanno Hildenbrandt [ctb] ,
Giovanni Laudanno [ctb]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 5.2.2 dated 2023-07-10 and 5.2.4 dated 2025-11-28
DESCRIPTION | 21 +- MD5 | 51 ++--- R/RcppExports.R | 7 R/bd_ML.R | 4 R/dd_KI_ML.R | 4 R/dd_LR.R | 4 R/dd_ML.R | 21 +- R/dd_MS_ML.R | 4 R/dd_SR_ML.R | 4 R/dd_loglik.R | 398 +++++++++++++++++++++------------------- R/dd_loglik_M.R | 3 R/dd_loglik_rhs.R | 15 + R/dd_utils.R | 112 +++++++---- build/partial.rdb |binary man/DDD-package.Rd | 7 man/bd_ML.Rd | 4 man/dd_KI_ML.Rd | 4 man/dd_LR.Rd | 4 man/dd_ML.Rd | 21 +- man/dd_MS_ML.Rd | 4 man/dd_SR_ML.Rd | 4 man/dd_loglik.Rd | 7 man/figures |only man/optimizer.Rd | 16 - man/simplex.Rd | 10 - src/RcppExports.cpp | 17 + src/dd_integrate_log_odeint.cpp |only 27 files changed, 444 insertions(+), 302 deletions(-)
Title: Write Reusable, Composable and Modular R Code
Description: A modern module system for R. Organise code into hierarchical,
composable, reusable modules, and use it effortlessly across projects via a
flexible, declarative dependency loading syntax.
Author: Konrad Rudolph [aut, cre] ,
Michael Schubert [ctb]
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>
Diff between box versions 1.2.0 dated 2024-02-06 and 1.2.1 dated 2025-11-28
box-1.2.0/box/inst/doc/mod-env-hierarchy.R |only box-1.2.0/box/inst/doc/mod-env-hierarchy.html |only box-1.2.0/box/inst/doc/mod-env-hierarchy.rmd |only box-1.2.0/box/src/unlock_env.c |only box-1.2.0/box/vignettes/environment-schema.png |only box-1.2.0/box/vignettes/mod-env-hierarchy.rmd |only box-1.2.1/box/DESCRIPTION | 13 +- box-1.2.1/box/LICENSE | 2 box-1.2.1/box/MD5 | 103 +++++++++--------- box-1.2.1/box/NEWS.md | 12 ++ box-1.2.1/box/R/display-help.r | 2 box-1.2.1/box/R/env.r | 4 box-1.2.1/box/R/loaded.r | 6 - box-1.2.1/box/R/use.r | 83 +++++++++++--- box-1.2.1/box/build/vignette.rds |binary box-1.2.1/box/inst/doc/box.R | 98 ++++++++--------- box-1.2.1/box/inst/doc/box.html | 29 ++--- box-1.2.1/box/inst/doc/box.rmd | 16 +- box-1.2.1/box/inst/doc/c/Makevars | 2 box-1.2.1/box/inst/doc/c/__setup__.r | 3 box-1.2.1/box/inst/doc/compiled-code.R | 51 ++++----- box-1.2.1/box/inst/doc/compiled-code.html | 20 +-- box-1.2.1/box/inst/doc/compiled-code.rmd | 5 box-1.2.1/box/inst/doc/contributing.R | 4 box-1.2.1/box/inst/doc/contributing.html | 7 - box-1.2.1/box/inst/doc/faq.R | 4 box-1.2.1/box/inst/doc/faq.html | 11 + box-1.2.1/box/inst/doc/faq.rmd | 4 box-1.2.1/box/inst/doc/migration.R | 112 ++++++++++---------- box-1.2.1/box/inst/doc/migration.html | 7 - box-1.2.1/box/inst/doc/mod-envs.R |only box-1.2.1/box/inst/doc/mod-envs.html |only box-1.2.1/box/inst/doc/mod-envs.rmd |only box-1.2.1/box/inst/doc/related.html | 6 - box-1.2.1/box/inst/doc/related.rmd | 2 box-1.2.1/box/inst/doc/testing.R | 42 +++---- box-1.2.1/box/inst/doc/testing.html | 7 - box-1.2.1/box/man/importing.Rd | 10 + box-1.2.1/box/man/use.Rd | 11 + box-1.2.1/box/src/exports.c | 2 box-1.2.1/box/tests/testthat/mod/reload/nested |only box-1.2.1/box/tests/testthat/support/run-shiny.r | 2 box-1.2.1/box/tests/testthat/test-basic.r | 5 box-1.2.1/box/tests/testthat/test-cyclic.r | 17 ++- box-1.2.1/box/tests/testthat/test-env.r | 2 box-1.2.1/box/tests/testthat/test-file.r | 2 box-1.2.1/box/tests/testthat/test-relative-import.r | 12 ++ box-1.2.1/box/tests/testthat/test-reload.r | 19 ++- box-1.2.1/box/tests/testthat/test-vignettes.r | 8 - box-1.2.1/box/tests/testthat/test-z-attach.r | 10 + box-1.2.1/box/vignettes/box.rmd | 16 +- box-1.2.1/box/vignettes/c/Makevars | 2 box-1.2.1/box/vignettes/c/__setup__.r | 3 box-1.2.1/box/vignettes/compiled-code.rmd | 5 box-1.2.1/box/vignettes/faq.rmd | 4 box-1.2.1/box/vignettes/mod-envs.rmd |only box-1.2.1/box/vignettes/related.rmd | 2 57 files changed, 457 insertions(+), 330 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-05 1.17.1
2022-02-26 1.17
2021-08-22 1.16
2021-06-26 1.15
2021-03-17 1.14
2021-01-04 1.13
2020-10-19 1.12
2020-07-23 1.11
2020-07-10 1.10
2020-07-01 1.9
2020-06-02 1.8
2020-03-18 1.7
2020-03-04 1.6
2020-02-21 1.5
2019-12-06 1.4
2019-09-18 1.3
2019-06-12 1.2
2019-05-06 1.1
2019-04-01 1.0
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Shawn Garbett [cre, ctb] ,
Jeremy Stephens [aut, ctb],
Kirill Simonov [aut],
Yihui Xie [ctb] ,
Zhuoer Dong [ctb],
Hadley Wickham [ctb] ,
Jeffrey Horner [ctb],
reikoch [ctb],
Will Beasley [ctb] ,
Brendan O'Connor [ctb],
Michael Quinn [ctb],
Charlie Ga [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between yaml versions 2.3.10 dated 2024-07-26 and 2.3.11 dated 2025-11-28
COPYING | 3 +-- DESCRIPTION | 48 ++++++++++++++++++++++++++++++++++++++++-------- LICENSE | 6 +++--- MD5 | 12 ++++++------ inst/CHANGELOG | 5 +++++ src/emitter.c | 18 +++++++++--------- src/r_emit.c | 1 - 7 files changed, 64 insertions(+), 29 deletions(-)
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>),
and grammatical differential evolution (O'Neill, M. and Brabazon, A. (2006) in
Arabinia, H. (2006, ISBN:978-193-241596-3).
All algorithms reuse basic adaptive mechanisms for performance optimization.
For xega's architecture, see Geyer [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.17 dated 2025-08-22 and 0.9.0.18 dated 2025-11-28
DESCRIPTION | 9 +++++---- MD5 | 9 +++++---- NEWS | 16 ++++++++++++++-- R/xegaRun.R | 18 ++++++------------ R/xegaVersion.R | 4 ++-- inst |only 6 files changed, 32 insertions(+), 24 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph]
,
Milan Straka [aut, cph] ,
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.13 dated 2025-11-26 and 0.8.15 dated 2025-11-28
DESCRIPTION | 27 +++++++++--------- MD5 | 24 ++++++++-------- NEWS.md | 8 +++++ inst/doc/udpipe-annotation.html | 6 ++-- inst/doc/udpipe-parallel.html | 6 ++-- inst/doc/udpipe-train.html | 6 ++-- inst/doc/udpipe-tryitout.html | 4 +- inst/doc/udpipe-universe.html | 4 +- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 4 +- inst/doc/udpipe-usecase-topicmodelling.html | 4 +- src/Makevars | 1 src/RcppExports.cpp | 5 +++ src/udpipe.cpp | 16 +++++++++- 13 files changed, 70 insertions(+), 45 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.1.2 dated 2025-11-24 and 3.1.4 dated 2025-11-28
DESCRIPTION | 10 - MD5 | 40 ++-- NEWS | 3 R/SVEMnet.R | 207 ++++++++++++++++----- R/bigexp.R | 298 +++++++++++++++++++++++-------- R/lipid_screen.R | 11 - R/select_candidates.R | 65 +++++- R/svem_random_table_multi.R | 271 ++++++++++++++++++++++------ R/svem_select_score_from_table.R | 5 R/svem_significance_test_parallel.R | 6 R/svem_wmt_multi.R | 36 ++- data/lipid_screen.rda |binary man/SVEMnet.Rd | 112 +++++++---- man/bigexp_terms.Rd | 96 ++++++--- man/bigexp_train.Rd | 2 man/lipid_screen.Rd | 11 - man/print.bigexp_spec.Rd | 42 ++++ man/svem_random_table_multi.Rd | 85 +++++++- man/svem_select_from_score_table.Rd | 1 man/svem_significance_test_parallel.Rd | 5 tests/testthat/test-random-table-multi.R | 62 ++++++ 21 files changed, 1054 insertions(+), 314 deletions(-)
Title: Approximate Summation of Series
Description: Application of theoretical results which ensure that the summation
of an infinite discrete series is within an arbitrary margin of error of its
true value. The C code under the hood is shared through header files to allow
users to sum their own low level functions as well. Based on the paper by
Braden (1992) <doi: 10.2307/2324995>.
Author: Guido A. Moreira [cre, aut] ,
Luiz Max Carvalho [ctb]
Maintainer: Guido A. Moreira <guidoalber@gmail.com>
This is a re-admission after prior archival of version 0.4.15 dated 2023-11-28
Diff between sumR versions 0.4.15 dated 2023-11-28 and 0.4.16 dated 2025-11-28
DESCRIPTION | 16 +++++++++------- MD5 | 22 +++++++++++----------- R/batches.R | 6 ++++-- R/finiteSum.R | 5 +++-- R/infiniteSum.R | 6 ++++-- man/finiteSum.Rd | 5 +++-- man/infiniteSum.Rd | 6 ++++-- man/infiniteSum_batches.Rd | 6 ++++-- man/precompiled.Rd | 4 ++-- man/sumR.Rd | 2 +- src/infiniteErrorBoundingPairs.c | 24 +++++++++++++----------- src/r_wrappers.h | 2 +- 12 files changed, 59 insertions(+), 45 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.2.8 dated 2025-10-02 and 0.2.10 dated 2025-11-28
DESCRIPTION | 6 ++-- MD5 | 44 ++++++++++++++--------------- NEWS.md | 8 +++++ R/Get_DB_MIUR.R | 14 +++++++-- R/Get_Registry.R | 59 +++++++++++++++++++++++----------------- R/Get_School2mun.R | 23 ++++++++++----- R/Get_nstud.R | 2 - R/Get_nteachers_prov.R | 49 +++++++++++++++++++++------------ R/Util_BroadBand2mun.R | 16 +++++++--- R/example_School2mun23.R | 10 ++++-- R/example_input_DB23_MIUR.R | 14 ++++++--- R/example_input_Registry23.R | 2 - R/example_input_nstud23.R | 2 - README.md | 2 - man/Get_DB_MIUR.Rd | 2 - man/Get_Registry.Rd | 2 - man/Get_School2mun.Rd | 8 +++-- man/Get_nstud.Rd | 2 - man/Get_nteachers_prov.Rd | 22 ++++++++++---- man/example_School2mun23.Rd | 9 ++++-- man/example_input_DB23_MIUR.Rd | 13 ++++++-- man/example_input_Registry23.Rd | 2 - man/example_input_nstud23.Rd | 2 - 23 files changed, 199 insertions(+), 114 deletions(-)
Title: Access the 'PREDICTS' Biodiversity Database
Description: Fetches the 'PREDICTS' database and relevant metadata from the Data
Portal at the Natural History Museum, London <https://data.nhm.ac.uk>. Data
were collated from over 400 existing spatial comparisons of local-scale
biodiversity exposed to different intensities and types of anthropogenic
pressures, from sites around the world. These data are described in Hudson
et al. (2013) <doi:10.1002/ece3.2579>.
Author: Connor Duffin [aut, cre],
The Trustees of The Natural History Museum, London [cph]
Maintainer: Connor Duffin <connor.p.duffin@gmail.com>
Diff between predictsr versions 0.1.1 dated 2025-07-23 and 0.2.0 dated 2025-11-28
predictsr-0.1.1/predictsr/R/predictsr.R |only predictsr-0.2.0/predictsr/DESCRIPTION | 13 - predictsr-0.2.0/predictsr/MD5 | 41 ++- predictsr-0.2.0/predictsr/NAMESPACE | 1 predictsr-0.2.0/predictsr/NEWS.md | 5 predictsr-0.2.0/predictsr/R/get-extras.R |only predictsr-0.2.0/predictsr/R/get-predicts-data.R |only predictsr-0.2.0/predictsr/R/load-predicts-data.R |only predictsr-0.2.0/predictsr/R/utils.R |only predictsr-0.2.0/predictsr/R/zzz.R | 2 predictsr-0.2.0/predictsr/README.md | 30 ++ predictsr-0.2.0/predictsr/inst/doc/predictsr.R | 10 predictsr-0.2.0/predictsr/inst/doc/predictsr.Rmd | 38 ++- predictsr-0.2.0/predictsr/inst/doc/predictsr.html | 114 +++++----- predictsr-0.2.0/predictsr/man/GetColumnDescriptions.Rd | 2 predictsr-0.2.0/predictsr/man/GetPredictsData.Rd | 2 predictsr-0.2.0/predictsr/man/GetSitelevelSummaries.Rd | 2 predictsr-0.2.0/predictsr/man/LoadPredictsData.Rd |only predictsr-0.2.0/predictsr/man/dot-IsValidPredictsData.Rd |only predictsr-0.2.0/predictsr/man/dot-ReadPredictsFileCache.Rd |only predictsr-0.2.0/predictsr/man/dot-WritePredictsFileCache.Rd |only predictsr-0.2.0/predictsr/man/predictsr-package.Rd | 1 predictsr-0.2.0/predictsr/tests/testthat/helper.R |only predictsr-0.2.0/predictsr/tests/testthat/test-load-predicts.R |only predictsr-0.2.0/predictsr/tests/testthat/test-predicts.R | 48 ---- predictsr-0.2.0/predictsr/tests/testthat/test-site-level.R | 70 ------ predictsr-0.2.0/predictsr/vignettes/predictsr.Rmd | 38 ++- 27 files changed, 207 insertions(+), 210 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.6.2 dated 2025-10-04 and 11.6.3 dated 2025-11-28
DESCRIPTION | 8 MD5 | 52 ++--- R/ANOVA.R | 27 ++ R/Dependence.R | 15 - R/Nowcast.R | 3 R/RcppExports.R | 8 R/Seasonality_Test.R | 192 ++++++------------ R/Uni_Causation.R | 3 R/gvload.R | 2 README.md | 4 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 2 inst/doc/NNSvignette_Clustering_and_Regression.html | 3 inst/doc/NNSvignette_Forecasting.html | 18 - inst/doc/NNSvignette_Overview.R | 13 - inst/doc/NNSvignette_Overview.Rmd | 30 +- inst/doc/NNSvignette_Overview.html | 110 ++++------ man/NNS.ANOVA.Rd | 23 ++ man/NNS.nowcast.Rd | 1 src/NNS_part.cpp | 5 src/NNS_seas.cpp |only src/RcppExports.cpp | 14 + src/central_tendencies.cpp | 5 src/central_tendencies.h |only src/partial_moments.h | 204 ++++++++++---------- src/partial_moments_rcpp.h | 91 +++++--- tests/testthat/Rplots.pdf |binary vignettes/NNSvignette_Clustering_and_Regression.Rmd | 2 vignettes/NNSvignette_Overview.Rmd | 30 +- 28 files changed, 461 insertions(+), 404 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 1.0 dated 2025-05-20 and 1.0.1 dated 2025-11-28
DESCRIPTION | 6 +- MD5 | 56 +++++++++---------- README.md | 2 inst/doc/README.R | 115 +++++++++++++++++++++------------------ inst/doc/README.html | 29 +++++---- man/figures/README-AdjSD-1.png |binary man/figures/README-BPI-1.png |binary man/figures/README-DMV-1.png |binary man/figures/README-RIE-1.png |binary man/figures/README-RP-1.png |binary man/figures/README-SAPA-1.png |binary man/figures/README-SlpAsp-1.png |binary man/figures/README-TPI-1.png |binary man/figures/README-Topo-1.png |binary man/figures/README-VRM-1.png |binary man/figures/qmetrics.jpg |binary man/figures/sub_qfit01.png |binary man/figures/sub_qfit02.png |binary man/figures/sub_qfit03.png |binary man/figures/sub_qfit04.png |binary man/figures/sub_qfit05.png |binary man/figures/sub_qfit06.png |binary man/figures/sub_qfit07.png |binary man/figures/sub_qfit08.png |binary man/figures/sub_qfit09.png |binary man/figures/sub_qfit10.png |binary man/figures/sub_qfit11.png |binary man/figures/sub_qfit12.png |binary man/fragments/README_Frag.Rmd | 117 +++++++++++++++++++++------------------- 29 files changed, 173 insertions(+), 152 deletions(-)
Title: Generate Recursive Mazes
Description: Supports the generation of parallelogram, equilateral
triangle, regular hexagon, isosceles trapezoid, Koch snowflake,
'hexaflake', Sierpinski triangle, Sierpinski carpet and Sierpinski
trapezoid mazes via 'TurtleGraphics'. Mazes are generated by the recursive method:
the domain is divided into sub-domains in which mazes are generated,
then dividing lines with holes are drawn between them, see
J. Buck, Recursive Division, <http://weblog.jamisbuck.org/2011/1/12/maze-generation-recursive-division-algorithm>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between mazealls versions 0.2.0 dated 2017-12-12 and 0.2.1 dated 2025-11-28
ChangeLog | 5 DESCRIPTION | 17 MD5 | 77 ++- NAMESPACE | 1 R/decagon_maze.r | 2 R/dodecagon_maze.r | 2 R/eq_triangle_maze.r | 12 R/hexaflake_maze.r | 5 R/hexagon_maze.r | 6 R/iso_trapezoid_maze.r | 4 R/koch_maze.r | 2 R/mazealls.r | 13 R/octagon_maze.r | 2 R/parallelogram_maze.r | 90 ++++ R/sierpinski_carpet_maze.r | 1 R/sierpinski_hexagon_maze.r |only R/sierpinski_maze.r | 3 R/sierpinski_trapezoid_maze.r | 3 R/utils.r | 9 README.md | 676 ++++++++++++++++++++++------------- inst/CITATION | 23 - man/NEWS.Rd | 9 man/decagon_maze.Rd | 23 - man/dodecagon_maze.Rd | 23 - man/eq_triangle_maze.Rd | 34 + man/figures/christmas-tree-1.png |only man/figures/para-hilbert-1.png |only man/figures/sierpinski-hexagon-1.png |only man/hexaflake_maze.Rd | 23 - man/hexagon_maze.Rd | 29 - man/holey_line.Rd | 10 man/holey_path.Rd | 12 man/iso_trapezoid_maze.Rd | 26 - man/koch_maze.Rd | 19 man/mazealls.Rd | 17 man/octagon_maze.Rd | 23 - man/parallelogram_maze.Rd | 54 ++ man/sierpinski_carpet_maze.Rd | 28 + man/sierpinski_hexagon_maze.Rd |only man/sierpinski_maze.Rd | 26 - man/sierpinski_trapezoid_maze.Rd | 26 - tests/testthat/test-basic.r | 48 +- 42 files changed, 945 insertions(+), 438 deletions(-)
Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching.
Core functionality includes automated training of emulators to data, diagnostic functions
to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
For details on the mathematical background, there are many papers available on the topic
(see references attached to function help files or the below references); for details of
the functions in this package, consult the manual or help files.
Iskauskas, A, et al. (2024) <doi:10.18637/jss.v109.i10>.
Bower, R.G., Goldstein, M., and Vernon, I. (2010) <doi:10.1214/10-BA524>.
Craig, P.S., Goldstein, M., Seheult, A.H., and Smith, J.A. (1997) <doi:10.1007/978-1-4612-2290-3_2>.
Author: Andrew Iskauskas [aut, cre] ,
TJ McKinley [aut]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>
Diff between hmer versions 1.6.0 dated 2024-05-31 and 1.6.2 dated 2025-11-28
DESCRIPTION | 15 MD5 | 48 +- NAMESPACE | 9 NEWS.md | 19 + R/Emulator.R | 103 ++++- R/Proto_emulator.R | 29 + R/VarianceEmulator.R | 157 ++++++-- R/diagnostics.R | 5 R/genpoints.R | 49 ++ R/implausibility.R | 2 R/modelbuilding.R | 3 R/multiwaveplot.R | 95 +++-- R/utils.R | 235 +++++++++++++ README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/demonstrating-the-hmer-package.html | 162 ++++----- inst/doc/emulationhandbook.html | 33 - inst/doc/low-dimensional-examples.html | 483 +++++++++++++-------------- inst/doc/stochasticandbimodalemulation.html | 80 ++-- man/export_emulator_to_json.Rd |only man/generate_new_design.Rd | 3 man/hit_by_wave.Rd | 12 man/import_emulator_from_json.Rd |only man/maximin_sample.Rd |only man/prin_vars.Rd |only tests/testthat/test-proto_em.R | 12 27 files changed, 1017 insertions(+), 544 deletions(-)
Title: The Gumbel-Hougaard Copula
Description: Provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Christophe Dutang [aut, cre] ,
Anne-Lise Caillat [ctb],
Veronique Larrieu [ctb],
Triet Nguyen [ctb]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between gumbel versions 1.10-3 dated 2024-10-17 and 1.10-4 dated 2025-11-28
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/gumbel.Rnw | 34 +++++++--------------------------- inst/doc/gumbel.pdf |binary vignettes/gumbel.Rnw | 34 +++++++--------------------------- 7 files changed, 26 insertions(+), 65 deletions(-)
Title: Ecological Stability Metrics
Description: Standardises and facilitates the use of eleven established stability properties that have been used to assess systems’ responses to press or pulse disturbances at different ecological levels (e.g. population, community). There are two sets of functions. The first set corresponds to functions that measure stability at any level of organisation, from individual to community and can be applied to a time series of a system’s state variables (e.g., body mass, population abundance, or species diversity). The properties included in this set are: invariability, resistance, extent and rate of recovery, persistence, and overall ecological vulnerability. The second set of functions can be applied to Jacobian matrices. The functions in this set measure the stability of a community at short and long time scales. In the short term, the community’s response is measured by maximal amplification, reactivity and initial resilience (i.e. initial rate of return to equilibrium). In the long term, stability [...truncated...]
Author: Ludmilla Figueiredo [aut, cre] ,
Viktoriia Radchuk [aut] ,
Cedric Scherer [ctb]
Maintainer: Ludmilla Figueiredo <ludmilla.figueiredo@protonmail.com>
Diff between estar versions 1.0-0 dated 2025-11-21 and 1.0-1 dated 2025-11-28
estar-1.0-0/estar/inst/doc/functional_metrics.R |only estar-1.0-0/estar/inst/doc/functional_metrics.Rmd |only estar-1.0-0/estar/inst/doc/functional_metrics.html |only estar-1.0-0/estar/inst/doc/jacobian_metrics.R |only estar-1.0-0/estar/inst/doc/jacobian_metrics.Rmd |only estar-1.0-0/estar/inst/doc/jacobian_metrics.html |only estar-1.0-0/estar/man/figures/logo.png |only estar-1.0-0/estar/vignettes/figures/multivar_benchmark.png |only estar-1.0-0/estar/vignettes/figures/univariate_metrics.png |only estar-1.0-0/estar/vignettes/functional_metrics.Rmd |only estar-1.0-0/estar/vignettes/jacobian_metrics.Rmd |only estar-1.0-1/estar/DESCRIPTION | 6 - estar-1.0-1/estar/MD5 | 39 ++++------ estar-1.0-1/estar/README.md | 5 + estar-1.0-1/estar/build/vignette.rds |binary estar-1.0-1/estar/inst/doc/functional_stability_properties.R |only estar-1.0-1/estar/inst/doc/functional_stability_properties.Rmd |only estar-1.0-1/estar/inst/doc/functional_stability_properties.html |only estar-1.0-1/estar/inst/doc/jacobian_stability_properties.R |only estar-1.0-1/estar/inst/doc/jacobian_stability_properties.Rmd |only estar-1.0-1/estar/inst/doc/jacobian_stability_properties.html |only estar-1.0-1/estar/man/figures/hex_sticker.png |only estar-1.0-1/estar/vignettes/figures/extent_recovery.png |binary estar-1.0-1/estar/vignettes/figures/invariability.png |binary estar-1.0-1/estar/vignettes/figures/jacobian_benchmark.png |only estar-1.0-1/estar/vignettes/figures/oev.png |binary estar-1.0-1/estar/vignettes/figures/persistence.png |binary estar-1.0-1/estar/vignettes/figures/rate_recovery.png |binary estar-1.0-1/estar/vignettes/figures/resistance.png |binary estar-1.0-1/estar/vignettes/functional_stability_properties.Rmd |only estar-1.0-1/estar/vignettes/jacobian_stability_properties.Rmd |only 31 files changed, 27 insertions(+), 23 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 1.3.2 dated 2025-07-23 and 1.4.0 dated 2025-11-28
cheapr-1.3.2/cheapr/R/cheapr_table.R |only cheapr-1.3.2/cheapr/R/zlegacy.R |only cheapr-1.3.2/cheapr/man/cheapr_if_else.Rd |only cheapr-1.3.2/cheapr/man/cheapr_table.Rd |only cheapr-1.3.2/cheapr/tests/testthat/test-new_df.R |only cheapr-1.4.0/cheapr/DESCRIPTION | 11 cheapr-1.4.0/cheapr/MD5 | 172 + cheapr-1.4.0/cheapr/NAMESPACE | 43 cheapr-1.4.0/cheapr/NEWS.md | 97 + cheapr-1.4.0/cheapr/R/as_discrete.R | 4 cheapr-1.4.0/cheapr/R/attrs.R | 17 cheapr-1.4.0/cheapr/R/case.R | 71 cheapr-1.4.0/cheapr/R/cast.R |only cheapr-1.4.0/cheapr/R/combine.R | 26 cheapr-1.4.0/cheapr/R/counts.R |only cheapr-1.4.0/cheapr/R/cpp11.R | 862 +++++----- cheapr-1.4.0/cheapr/R/cpp_rebuild.R |only cheapr-1.4.0/cheapr/R/data_frame.R | 30 cheapr-1.4.0/cheapr/R/extras.R | 155 - cheapr-1.4.0/cheapr/R/factors.R | 12 cheapr-1.4.0/cheapr/R/gcd.R | 1 cheapr-1.4.0/cheapr/R/if_else.R | 59 cheapr-1.4.0/cheapr/R/int64.R | 2 cheapr-1.4.0/cheapr/R/is_whole_number.R |only cheapr-1.4.0/cheapr/R/lists.R | 4 cheapr-1.4.0/cheapr/R/na_init.R |only cheapr-1.4.0/cheapr/R/overview.R | 23 cheapr-1.4.0/cheapr/R/paste.R |only cheapr-1.4.0/cheapr/R/rebuild.R | 91 - cheapr-1.4.0/cheapr/R/recycle.R | 5 cheapr-1.4.0/cheapr/R/rep.R | 11 cheapr-1.4.0/cheapr/R/replace.R |only cheapr-1.4.0/cheapr/R/scalars.R | 12 cheapr-1.4.0/cheapr/R/sequences.R | 211 +- cheapr-1.4.0/cheapr/R/sset.R | 111 - cheapr-1.4.0/cheapr/R/str_coalesce.R | 6 cheapr-1.4.0/cheapr/R/switch_args.R |only cheapr-1.4.0/cheapr/R/unique.R |only cheapr-1.4.0/cheapr/R/utils.R | 45 cheapr-1.4.0/cheapr/README.md | 859 +++++++-- cheapr-1.4.0/cheapr/inst/include/cheapr_api.h | 192 +- cheapr-1.4.0/cheapr/inst/include/core.h |only cheapr-1.4.0/cheapr/man/as_discrete.Rd | 2 cheapr-1.4.0/cheapr/man/attrs.Rd | 4 cheapr-1.4.0/cheapr/man/case.Rd | 2 cheapr-1.4.0/cheapr/man/cast.Rd |only cheapr-1.4.0/cheapr/man/cheapr_c.Rd | 25 cheapr-1.4.0/cheapr/man/counts.Rd |only cheapr-1.4.0/cheapr/man/cpp_rebuild.Rd |only cheapr-1.4.0/cheapr/man/data_frame.Rd | 4 cheapr-1.4.0/cheapr/man/extras.Rd | 69 cheapr-1.4.0/cheapr/man/figures/README-unnamed-chunk-52-1.png |only cheapr-1.4.0/cheapr/man/figures/README-unnamed-chunk-52-2.png |only cheapr-1.4.0/cheapr/man/figures/README-unnamed-chunk-57-1.png |only cheapr-1.4.0/cheapr/man/figures/README-unnamed-chunk-57-2.png |only cheapr-1.4.0/cheapr/man/gcd.Rd | 1 cheapr-1.4.0/cheapr/man/if_else.Rd |only cheapr-1.4.0/cheapr/man/is_whole_number.Rd |only cheapr-1.4.0/cheapr/man/lists.Rd | 4 cheapr-1.4.0/cheapr/man/na_init.Rd |only cheapr-1.4.0/cheapr/man/rebuild.Rd | 6 cheapr-1.4.0/cheapr/man/recycle.Rd | 4 cheapr-1.4.0/cheapr/man/rep.Rd | 11 cheapr-1.4.0/cheapr/man/replace.Rd |only cheapr-1.4.0/cheapr/man/sequences.Rd | 99 - cheapr-1.4.0/cheapr/man/sset.Rd | 47 cheapr-1.4.0/cheapr/man/str_coalesce.Rd | 6 cheapr-1.4.0/cheapr/man/strings.Rd |only cheapr-1.4.0/cheapr/man/switch_args.Rd |only cheapr-1.4.0/cheapr/man/unique_.Rd |only cheapr-1.4.0/cheapr/src/Makevars | 2 cheapr-1.4.0/cheapr/src/Makevars.win |only cheapr-1.4.0/cheapr/src/altrep.cpp | 16 cheapr-1.4.0/cheapr/src/api.cpp | 136 + cheapr-1.4.0/cheapr/src/attrs.cpp | 2 cheapr-1.4.0/cheapr/src/cast.cpp |only cheapr-1.4.0/cheapr/src/cast.h |only cheapr-1.4.0/cheapr/src/cheapr.h | 368 ---- cheapr-1.4.0/cheapr/src/combine.cpp | 695 +++----- cheapr-1.4.0/cheapr/src/conditions.cpp |only cheapr-1.4.0/cheapr/src/cpp11.cpp | 198 +- cheapr-1.4.0/cheapr/src/decls.h |only cheapr-1.4.0/cheapr/src/gcd.cpp | 154 - cheapr-1.4.0/cheapr/src/groups.cpp |only cheapr-1.4.0/cheapr/src/int64.cpp | 113 + cheapr-1.4.0/cheapr/src/lag.cpp | 95 - cheapr-1.4.0/cheapr/src/lists.cpp | 284 ++- cheapr-1.4.0/cheapr/src/nas.cpp | 229 +- cheapr-1.4.0/cheapr/src/replace.cpp |only cheapr-1.4.0/cheapr/src/scalars.cpp | 538 ------ cheapr-1.4.0/cheapr/src/sequences.cpp | 429 ++-- cheapr-1.4.0/cheapr/src/set_math.cpp | 304 ++- cheapr-1.4.0/cheapr/src/sset.cpp | 351 ++-- cheapr-1.4.0/cheapr/src/strings.cpp |only cheapr-1.4.0/cheapr/src/types.h |only cheapr-1.4.0/cheapr/src/utils.cpp | 858 +++------ cheapr-1.4.0/cheapr/src/variadic.h |only cheapr-1.4.0/cheapr/src/which.cpp | 689 +------ cheapr-1.4.0/cheapr/tests/testthat/_snaps/cast.md |only cheapr-1.4.0/cheapr/tests/testthat/_snaps/combine.md |only cheapr-1.4.0/cheapr/tests/testthat/_snaps/overview.md | 2 cheapr-1.4.0/cheapr/tests/testthat/test-case.R | 2 cheapr-1.4.0/cheapr/tests/testthat/test-cast.R |only cheapr-1.4.0/cheapr/tests/testthat/test-combine.R |only cheapr-1.4.0/cheapr/tests/testthat/test-data_frame.R |only cheapr-1.4.0/cheapr/tests/testthat/test-if_else.R | 40 cheapr-1.4.0/cheapr/tests/testthat/test-nas.R | 269 +-- cheapr-1.4.0/cheapr/tests/testthat/test-overview.R | 14 cheapr-1.4.0/cheapr/tests/testthat/test-sequences.R | 4 109 files changed, 4576 insertions(+), 4632 deletions(-)
Title: Client for the 'BAN' API
Description: A client for the 'Base Adresses Nationale' ('BAN') API, which allows to (batch)
geocode and reverse-geocode French addresses. For more information about the 'BAN' and its API, please see <https://adresse.data.gouv.fr/outils/api-doc/adresse>.
Author: Joel Gombin [cre, aut],
Paul-Antoine Chevalier [aut]
Maintainer: Joel Gombin <joel.gombin@gmail.com>
Diff between banR versions 0.2.3 dated 2025-11-24 and 0.2.4 dated 2025-11-28
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++---------- R/geocode.R | 5 +++- R/geocode_tbl.R | 6 +++-- inst/doc/geocode.html | 4 +-- man/geocode.Rd | 2 + man/geocode_tbl.Rd | 3 +- man/reverse_geocode.Rd | 3 +- man/reverse_geocode_tbl.Rd | 3 +- tests/testthat/test_geocode.R | 2 + tests/testthat/test_geocodetbl.R | 41 ++++++++++++++++++++++----------------- 11 files changed, 57 insertions(+), 38 deletions(-)
Title: Adaptive Double Sparse Iterative Hard Thresholding
Description: Solving high-dimensional double sparse linear regression via an iterative hard thresholding algorithm. Furthermore, the method is extended to jointly estimate multiple graphical models. For more details, please see <https://www.jmlr.org/papers/v25/23-0653.html> and <doi:10.48550/arXiv.2503.18722>.
Author: Yanhang Zhang [aut, cre],
Zhifan Li [aut],
Jianxin Yin [aut],
Shixiang Liu [aut],
Lingren Kong [aut]
Maintainer: Yanhang Zhang <zhangyh98@tsinghua.edu.cn>
This is a re-admission after prior archival of version 0.2.0 dated 2025-04-17
Diff between ADSIHT versions 0.2.0 dated 2025-04-17 and 0.2.1 dated 2025-11-28
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- build/partial.rdb |binary src/Data.h | 3 +++ 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Variational Bayes for Fast and Accurate Empirical Likelihood
Inference
Description: Computes the Gaussian variational approximation of the Bayesian
empirical likelihood posterior. This is an implementation of the function
found in Yu, W., & Bondell, H. D. (2023) <doi:10.1080/01621459.2023.2169701>.
Author: Weichang Yu [aut, cre] ,
Jeremy Lim [aut]
Maintainer: Weichang Yu <weichang.yu@unimelb.edu.au>
Diff between VBel versions 1.1.6 dated 2025-10-26 and 1.1.7 dated 2025-11-28
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NEWS.md | 4 ++++ build/partial.rdb |binary 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
Description: Rapid, simulation-based exact (restricted) likelihood ratio tests
for testing the presence of variance components/nonparametric terms for
models fit with nlme::lme(),lme4::lmer(), lmerTest::lmer(), gamm4::gamm4() and
mgcv::gamm().
Author: Fabian Scheipl [aut, cre] ,
Ben Bolker [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@stat.uni-muenchen.de>
Diff between RLRsim versions 3.1-8 dated 2022-03-16 and 3.1-9 dated 2025-11-28
DESCRIPTION | 18 ++++++------ MD5 | 8 ++--- R/extract.lmeDesign.R | 70 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary inst/CITATION | 36 ++++++++++++------------- 5 files changed, 66 insertions(+), 66 deletions(-)
Title: Wrapper of 'CDO' Operators
Description: Provides a translation layer between 'R' and 'CDO' operators. Each
operator is it's own function with documentation. Nested or piped functions
will be translated into 'CDO' chains.
Author: Elio Campitelli [cre, aut, cph] ,
MPI fuer Meteorologie [cph]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between rcdo versions 0.3.1 dated 2025-11-24 and 0.3.2 dated 2025-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/cdo.R | 14 ++++++++------ 4 files changed, 20 insertions(+), 12 deletions(-)
Title: A Toolkit for Sports Injury and Illness Data Analysis
Description: Sports Injury Data analysis aims to identify and describe the
magnitude of the injury problem, and to gain more insights (e.g.
determine potential risk factors) by statistical modelling approaches.
The 'injurytools' package provides standardized routines and utilities
that simplify such analyses. It offers functions for data preparation,
informative visualizations and descriptive and model-based analyses.
Author: Lore Zumeta Olaskoaga [aut, cre] ,
Dae-Jin Lee [ctb]
Maintainer: Lore Zumeta Olaskoaga <lorezumeta@gmail.com>
Diff between injurytools versions 1.0.3 dated 2023-11-14 and 2.0.0 dated 2025-11-28
injurytools-1.0.3/injurytools/R/gg_injbarplot.R |only injurytools-1.0.3/injurytools/R/gg_injphoto.R |only injurytools-1.0.3/injurytools/R/gg_injprev_polar.R |only injurytools-1.0.3/injurytools/R/gg_injriskmatrix.R |only injurytools-1.0.3/injurytools/R/injprev.R |only injurytools-1.0.3/injurytools/R/injsummary.R |only injurytools-1.0.3/injurytools/inst/WORDLIST |only injurytools-1.0.3/injurytools/man/gg_injbarplot.Rd |only injurytools-1.0.3/injurytools/man/gg_injphoto.Rd |only injurytools-1.0.3/injurytools/man/gg_injprev_polar.Rd |only injurytools-1.0.3/injurytools/man/gg_injriskmatrix.Rd |only injurytools-1.0.3/injurytools/man/injprev.Rd |only injurytools-1.0.3/injurytools/man/injsummary.Rd |only injurytools-1.0.3/injurytools/man/injsummary_unit.Rd |only injurytools-1.0.3/injurytools/man/is_injds.Rd |only injurytools-1.0.3/injurytools/tests/spelling.R |only injurytools-1.0.3/injurytools/tests/testthat/test-gg_injbarplot.R |only injurytools-1.0.3/injurytools/tests/testthat/test-gg_injphoto.R |only injurytools-1.0.3/injurytools/tests/testthat/test-gg_injprev_polar.R |only injurytools-1.0.3/injurytools/tests/testthat/test-gg_injriskmatrix.R |only injurytools-1.0.3/injurytools/tests/testthat/test-injprev.R |only injurytools-1.0.3/injurytools/tests/testthat/test-injsummary.R |only injurytools-2.0.0/injurytools/DESCRIPTION | 63 injurytools-2.0.0/injurytools/MD5 | 169 + injurytools-2.0.0/injurytools/NAMESPACE | 44 injurytools-2.0.0/injurytools/NEWS.md | 26 injurytools-2.0.0/injurytools/R/calc_burden.R |only injurytools-2.0.0/injurytools/R/calc_exposure.R |only injurytools-2.0.0/injurytools/R/calc_incidence.R |only injurytools-2.0.0/injurytools/R/calc_iqr_dayslost.R |only injurytools-2.0.0/injurytools/R/calc_mean_dayslost.R |only injurytools-2.0.0/injurytools/R/calc_median_dayslost.R |only injurytools-2.0.0/injurytools/R/calc_ncases.R |only injurytools-2.0.0/injurytools/R/calc_ndayslost.R |only injurytools-2.0.0/injurytools/R/calc_prevalence.R |only injurytools-2.0.0/injurytools/R/calc_summary.R |only injurytools-2.0.0/injurytools/R/data.R | 2 injurytools-2.0.0/injurytools/R/gg_photo.R |only injurytools-2.0.0/injurytools/R/gg_prevalence.R |only injurytools-2.0.0/injurytools/R/gg_rank.R |only injurytools-2.0.0/injurytools/R/gg_riskmatrix.R |only injurytools-2.0.0/injurytools/R/helpers.R | 85 injurytools-2.0.0/injurytools/R/injurytools-package.R | 2 injurytools-2.0.0/injurytools/R/prepare_data.R | 229 +- injurytools-2.0.0/injurytools/R/summary_unit.R |only injurytools-2.0.0/injurytools/R/sysdata.rda |binary injurytools-2.0.0/injurytools/R/utils.R | 108 - injurytools-2.0.0/injurytools/README.md | 78 injurytools-2.0.0/injurytools/build/partial.rdb |only injurytools-2.0.0/injurytools/build/vignette.rds |binary injurytools-2.0.0/injurytools/data/injd.rda |binary injurytools-2.0.0/injurytools/data/raw_df_exposures.rda |binary injurytools-2.0.0/injurytools/data/raw_df_injuries.rda |binary injurytools-2.0.0/injurytools/inst/doc/estimate-epi-measures.R | 274 +- injurytools-2.0.0/injurytools/inst/doc/estimate-epi-measures.Rmd | 152 - injurytools-2.0.0/injurytools/inst/doc/estimate-epi-measures.html | 937 +++------- injurytools-2.0.0/injurytools/inst/doc/model-injury-data-i.R | 194 +- injurytools-2.0.0/injurytools/inst/doc/model-injury-data-i.Rmd | 98 - injurytools-2.0.0/injurytools/inst/doc/model-injury-data-i.html | 301 +-- injurytools-2.0.0/injurytools/inst/doc/model-injury-data-ii.R | 254 +- injurytools-2.0.0/injurytools/inst/doc/model-injury-data-ii.Rmd | 56 injurytools-2.0.0/injurytools/inst/doc/model-injury-data-ii.html | 580 +++--- injurytools-2.0.0/injurytools/inst/doc/prepare-injury-data.R | 8 injurytools-2.0.0/injurytools/inst/doc/prepare-injury-data.Rmd | 18 injurytools-2.0.0/injurytools/inst/doc/prepare-injury-data.html | 79 injurytools-2.0.0/injurytools/inst/doc/visualize-injury-data.R | 517 ++--- injurytools-2.0.0/injurytools/inst/doc/visualize-injury-data.Rmd | 271 +- injurytools-2.0.0/injurytools/inst/doc/visualize-injury-data.html | 712 +++---- injurytools-2.0.0/injurytools/man/calc_burden.Rd |only injurytools-2.0.0/injurytools/man/calc_exposure.Rd |only injurytools-2.0.0/injurytools/man/calc_incidence.Rd |only injurytools-2.0.0/injurytools/man/calc_iqr_dayslost.Rd |only injurytools-2.0.0/injurytools/man/calc_mean_dayslost.Rd |only injurytools-2.0.0/injurytools/man/calc_median_dayslost.Rd |only injurytools-2.0.0/injurytools/man/calc_ncases.Rd |only injurytools-2.0.0/injurytools/man/calc_ndayslost.Rd |only injurytools-2.0.0/injurytools/man/calc_prevalence.Rd |only injurytools-2.0.0/injurytools/man/calc_summary.Rd |only injurytools-2.0.0/injurytools/man/check_injfollowup.Rd | 2 injurytools-2.0.0/injurytools/man/cut_injd.Rd | 4 injurytools-2.0.0/injurytools/man/data_followup.Rd | 4 injurytools-2.0.0/injurytools/man/data_injurieslong.Rd | 2 injurytools-2.0.0/injurytools/man/figures/README-unnamed-chunk-4-1.png |binary injurytools-2.0.0/injurytools/man/figures/README-unnamed-chunk-5-1.png |only injurytools-2.0.0/injurytools/man/figures/README-unnamed-chunk-6-1.png |only injurytools-2.0.0/injurytools/man/get_data_exposures.Rd |only injurytools-2.0.0/injurytools/man/get_data_followup.Rd |only injurytools-2.0.0/injurytools/man/get_data_injuries.Rd |only injurytools-2.0.0/injurytools/man/gg_photo.Rd |only injurytools-2.0.0/injurytools/man/gg_prevalence.Rd |only injurytools-2.0.0/injurytools/man/gg_rank.Rd |only injurytools-2.0.0/injurytools/man/gg_riskmatrix.Rd |only injurytools-2.0.0/injurytools/man/injd.Rd | 2 injurytools-2.0.0/injurytools/man/injurytools.Rd | 6 injurytools-2.0.0/injurytools/man/label_unit.Rd |only injurytools-2.0.0/injurytools/man/new_injd.Rd | 14 injurytools-2.0.0/injurytools/man/prepare_data.Rd | 40 injurytools-2.0.0/injurytools/man/summary_unit.Rd |only injurytools-2.0.0/injurytools/tests/testthat/_snaps/prepare_data.md | 2 injurytools-2.0.0/injurytools/tests/testthat/test-calc_burden.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_exposure.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_incidence.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_iqr_dayslost.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_mean_dayslost.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_median_dayslost.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_ncases.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_ndayslost.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_prevalence.R |only injurytools-2.0.0/injurytools/tests/testthat/test-calc_summary.R |only injurytools-2.0.0/injurytools/tests/testthat/test-gg_photo.R |only injurytools-2.0.0/injurytools/tests/testthat/test-gg_prevalence.R |only injurytools-2.0.0/injurytools/tests/testthat/test-gg_rank.R |only injurytools-2.0.0/injurytools/tests/testthat/test-gg_riskmatrix.R |only injurytools-2.0.0/injurytools/tests/testthat/test-gg_time_trend.R |only injurytools-2.0.0/injurytools/tests/testthat/test-helpers.R | 43 injurytools-2.0.0/injurytools/tests/testthat/test-prepare_data.R | 28 injurytools-2.0.0/injurytools/tests/testthat/test-summary_unit.R |only injurytools-2.0.0/injurytools/tests/testthat/test-utils.R | 50 injurytools-2.0.0/injurytools/vignettes/estimate-epi-measures.Rmd | 152 - injurytools-2.0.0/injurytools/vignettes/model-injury-data-i.Rmd | 98 - injurytools-2.0.0/injurytools/vignettes/model-injury-data-ii.Rmd | 56 injurytools-2.0.0/injurytools/vignettes/prepare-injury-data.Rmd | 18 injurytools-2.0.0/injurytools/vignettes/visualize-injury-data.Rmd | 271 +- 123 files changed, 2912 insertions(+), 3137 deletions(-)
Title: Regression under Network Interference
Description: An implementation of generalized linear models (GLMs) for studying relationships among attributes in connected populations, where responses of connected units can be dependent, as introduced by Fritz et al. (2025) <doi:10.1080/01621459.2025.2565851>. 'igml' extends GLMs for independent responses to dependent responses and can be used for studying spillover in connected populations and other network-mediated phenomena.
Author: Cornelius Fritz [aut, cre],
Michael Schweinberger [aut]
Maintainer: Cornelius Fritz <corneliusfritz2010@gmail.com>
Diff between iglm versions 1.0 dated 2025-11-25 and 1.1 dated 2025-11-28
iglm-1.0/iglm/man/iglm_object_generator.Rd |only iglm-1.0/iglm/man/model_terms.Rd |only iglm-1.0/iglm/man/results_generator.Rd |only iglm-1.0/iglm/man/sampler.net_attr.Rd |only iglm-1.0/iglm/man/sampler_iglm_generator.Rd |only iglm-1.0/iglm/man/sampler_net_attr_generator.Rd |only iglm-1.1/iglm/DESCRIPTION | 6 iglm-1.1/iglm/MD5 | 68 - iglm-1.1/iglm/NAMESPACE | 9 iglm-1.1/iglm/R/count_statistics.R | 2 iglm-1.1/iglm/R/estimation.R | 77 +- iglm-1.1/iglm/R/iglm.r | 281 ++++++- iglm-1.1/iglm/R/iglm_data.r | 35 iglm-1.1/iglm/R/results.r | 784 ++++++++++++++++----- iglm-1.1/iglm/R/sampler.r | 187 ++--- iglm-1.1/iglm/R/simulation.R | 45 - iglm-1.1/iglm/R/zzz.R | 154 ++++ iglm-1.1/iglm/inst/doc/iglm.R | 6 iglm-1.1/iglm/inst/doc/iglm.Rmd | 6 iglm-1.1/iglm/inst/doc/iglm.html | 11 iglm-1.1/iglm/inst/include/iglm/helper_functions.h | 13 iglm-1.1/iglm/man/count_statistics.Rd | 2 iglm-1.1/iglm/man/create_userterms_skeleton.Rd |only iglm-1.1/iglm/man/iglm.Rd | 20 iglm-1.1/iglm/man/iglm.object.generator.Rd |only iglm-1.1/iglm/man/model.terms.Rd |only iglm-1.1/iglm/man/results.generator.Rd |only iglm-1.1/iglm/man/sampler.iglm.Rd | 28 iglm-1.1/iglm/man/sampler.iglm.generator.Rd |only iglm-1.1/iglm/man/sampler.net.attr.Rd |only iglm-1.1/iglm/man/sampler.net.attr.generator.Rd |only iglm-1.1/iglm/man/simulate_iglm.Rd | 6 iglm-1.1/iglm/src/Makevars | 18 iglm-1.1/iglm/src/RcppExports.cpp | 2 iglm-1.1/iglm/src/change_statistics.cpp | 4 iglm-1.1/iglm/src/xyz_sampling.cpp | 49 + iglm-1.1/iglm/tests/testthat/Rplots.pdf |only iglm-1.1/iglm/tests/testthat/test-iglm.R | 25 iglm-1.1/iglm/tests/testthat/test-results.R | 7 iglm-1.1/iglm/tests/testthat/test-sampler.R | 36 iglm-1.1/iglm/tests/testthat/test-statistics.R | 15 iglm-1.1/iglm/vignettes/iglm.Rmd | 6 42 files changed, 1393 insertions(+), 509 deletions(-)
Title: Feldman-Cousins Confidence Intervals
Description: Provides support for building Feldman-Cousins confidence intervals
[G. J. Feldman and R. D. Cousins (1998) <doi:10.1103/PhysRevD.57.3873>].
Author: Valerio Gherardi [aut, cre]
Maintainer: Valerio Gherardi <vgherard840@gmail.com>
Diff between fcci versions 1.0.1 dated 2022-01-07 and 1.0.2 dated 2025-11-28
DESCRIPTION | 12 - MD5 | 41 +-- NAMESPACE | 14 - NEWS.md | 13 - R/RcppExports.R | 30 +- R/assertions.R | 100 ++++---- R/binom.R | 114 ++++----- R/fcci-package.R | 22 - R/pois.R | 324 ++++++++++++++-------------- README.md | 221 +++++++++---------- build |only man/confint_binom.Rd | 84 +++---- man/confint_pois.Rd | 190 ++++++++-------- man/fcci-package.Rd | 48 ++-- tests/testthat.R | 8 tests/testthat/test-algorithm_binom.R | 46 +-- tests/testthat/test-algorithm_pois.R | 98 ++++---- tests/testthat/test-check_args_binom.R | 110 ++++----- tests/testthat/test-check_args_pois.R | 178 +++++++-------- tests/testthat/test-check_truncation_pois.R | 86 +++---- tests/testthat/test-confint_binom.R | 42 +-- tests/testthat/test-confint_pois.R | 60 ++--- 22 files changed, 923 insertions(+), 918 deletions(-)
Title: Parsing, Applying, and Manipulating Data Cleaning Rules
Description: Please note: active development has moved to packages 'validate'
and 'errorlocate'. Facilitates reading and manipulating (multivariate) data
restrictions (edit rules) on numerical and categorical data. Rules can be
defined with common R syntax and parsed to an internal (matrix-like format).
Rules can be manipulated with variable elimination and value substitution
methods, allowing for feasibility checks and more. Data can be tested against
the rules and erroneous fields can be found based on Fellegi and Holt's
generalized principle. Rules dependencies can be visualized with using the
'igraph' package.
Author: Edwin de Jonge [aut, cre] ,
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between editrules versions 2.9.5 dated 2024-05-04 and 2.9.6 dated 2025-11-28
DESCRIPTION | 21 ++++++++++++++++----- MD5 | 20 ++++++++++---------- NEWS | 3 +++ R/errorLocalizer_mip.R | 2 +- R/pkg.R | 2 +- R/plot.R | 4 ++-- build/vignette.rds |binary inst/doc/editrules-vignette.pdf |binary man/as.lp.mip.Rd | 2 +- man/editrules.plotting.Rd | 4 ++-- man/editrules_package.Rd | 11 ++++++++++- 11 files changed, 46 insertions(+), 23 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.10 dated 2025-10-14 and 0.1.11 dated 2025-11-28
babelmixr2-0.1.10/babelmixr2/tests/testthat/bad-nonmem-data-convert.qs |only babelmixr2-0.1.11/babelmixr2/DESCRIPTION | 12 ++-- babelmixr2-0.1.11/babelmixr2/MD5 | 20 ++++---- babelmixr2-0.1.11/babelmixr2/NEWS.md | 4 + babelmixr2-0.1.11/babelmixr2/R/monolixNlmixr2est.R | 8 +-- babelmixr2-0.1.11/babelmixr2/R/monolixRxUiGet.R | 2 babelmixr2-0.1.11/babelmixr2/R/nonmemNlmixr2est.R | 4 - babelmixr2-0.1.11/babelmixr2/R/nonmemRxUiGet.R | 2 babelmixr2-0.1.11/babelmixr2/tests/testthat/bad-nonmem-data-convert.qs2 |only babelmixr2-0.1.11/babelmixr2/tests/testthat/test-convert.R | 4 - babelmixr2-0.1.11/babelmixr2/tests/testthat/test-monolix-read.R | 8 +-- babelmixr2-0.1.11/babelmixr2/tests/testthat/test-poped.R | 25 +++------- 12 files changed, 43 insertions(+), 46 deletions(-)
Title: Adirondack Long-Term Lake Data
Description: Package for the access and distribution of long-term lake datasets from lakes in the Adirondack Park, northern New York state. Includes a wide variety of physical, chemical, and biological parameters from 28 lakes. Data are from multiple collection organizations and have been harmonized in both time and space for ease of reuse.
Author: Jeremy Farrell [aut, cre],
Luke Winslow [aut],
Taylor Leach [aut],
Tobi Hahn [aut]
Maintainer: Jeremy Farrell <jeremyfarrell@gmail.com>
This is a re-admission after prior archival of version 0.6.1 dated 2018-02-16
Diff between adklakedata versions 0.6.1 dated 2018-02-16 and 0.6.4 dated 2025-11-28
adklakedata-0.6.1/adklakedata/demo |only adklakedata-0.6.4/adklakedata/DESCRIPTION | 39 +- adklakedata-0.6.4/adklakedata/LICENSE | 2 adklakedata-0.6.4/adklakedata/MD5 | 50 +- adklakedata-0.6.4/adklakedata/NAMESPACE | 30 - adklakedata-0.6.4/adklakedata/R/aaa.R | 8 adklakedata-0.6.4/adklakedata/R/adk_data.R | 23 - adklakedata-0.6.4/adklakedata/R/adk_lake_shapes.R | 89 ++--- adklakedata-0.6.4/adklakedata/R/adk_lakes.R | 8 adklakedata-0.6.4/adklakedata/R/adk_metadata.R | 44 +- adklakedata-0.6.4/adklakedata/R/check_dl_data.R | 168 +++++----- adklakedata-0.6.4/adklakedata/R/check_dl_file.R | 144 ++++---- adklakedata-0.6.4/adklakedata/inst/extdata/BlueLine2014Poly.shp.xml | 72 ++-- adklakedata-0.6.4/adklakedata/inst/extdata/master.csv | 4 adklakedata-0.6.4/adklakedata/inst/extdata/metadata/nldas_drivers_1979_2016.txt | 20 - adklakedata-0.6.4/adklakedata/man/adk_data.Rd | 2 adklakedata-0.6.4/adklakedata/man/adk_lake_shapes.Rd | 9 adklakedata-0.6.4/adklakedata/man/adk_lakes.Rd | 5 adklakedata-0.6.4/adklakedata/man/adk_metadata.Rd | 42 +- adklakedata-0.6.4/adklakedata/man/adk_shape.Rd | 8 adklakedata-0.6.4/adklakedata/man/check_dl_data.Rd | 34 +- adklakedata-0.6.4/adklakedata/man/check_dl_file.Rd | 3 adklakedata-0.6.4/adklakedata/man/local_path.Rd | 48 +- adklakedata-0.6.4/adklakedata/man/set_local_path.Rd | 44 +- adklakedata-0.6.4/adklakedata/tests/testthat.R | 8 adklakedata-0.6.4/adklakedata/tests/testthat/test_data_dl_access.R | 62 +-- 26 files changed, 483 insertions(+), 483 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-23 1.2.3
2022-07-07 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-15 0.5.0
2022-01-04 0.4.1
2021-09-17 0.4.0
2020-09-30 0.3.0
2020-01-17 0.2.0
2019-10-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-05 0.3.12
2022-11-03 0.3.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-20 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-23 0.1.5
2021-10-29 0.1.4
2020-03-29 0.1.3
2020-01-25 0.1.2
2018-09-15 0.1.1
2018-05-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-16 1.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-18 0.5.7
2022-11-14 0.5.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-28 1.2.4
Title: Assessing Package Risk Metrics
Description: A reliable and validated tool that captures detailed risk metrics
such as R 'CMD' check, test coverage, traceability matrix, documentation, dependencies,
reverse dependencies, suggested dependency analysis, repository data,
and enhanced reporting for R packages that are local or stored
on remote repositories such as GitHub, CRAN, and Bioconductor.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between risk.assessr versions 2.0.1 dated 2025-08-22 and 3.0.0 dated 2025-11-28
risk.assessr-2.0.1/risk.assessr/R/create_risk_profile.R |only risk.assessr-2.0.1/risk.assessr/R/create_weights_profile.R |only risk.assessr-2.0.1/risk.assessr/R/update_pscore_results.R |only risk.assessr-2.0.1/risk.assessr/R/update_results_doc_scores.R |only risk.assessr-2.0.1/risk.assessr/inst/doc/create-your-weights-profile.R |only risk.assessr-2.0.1/risk.assessr/inst/doc/create-your-weights-profile.Rmd |only risk.assessr-2.0.1/risk.assessr/inst/doc/create-your-weights-profile.html |only risk.assessr-2.0.1/risk.assessr/inst/test-data/haven-2.5.4.tar.gz |only risk.assessr-2.0.1/risk.assessr/man/add_default_risk_weights.Rd |only risk.assessr-2.0.1/risk.assessr/man/assess_dep_for_sigmoid.Rd |only risk.assessr-2.0.1/risk.assessr/man/calc_dependencies.Rd |only risk.assessr-2.0.1/risk.assessr/man/calc_overall_risk_score.Rd |only risk.assessr-2.0.1/risk.assessr/man/calc_reverse_dependencies.Rd |only risk.assessr-2.0.1/risk.assessr/man/calc_risk_profile.Rd |only 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-11 1.8.0
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2019-03-12 1.5.0
2015-11-21 1.4
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Title: Simple Features for R
Description: Support for simple feature access, a standardized way to
encode and analyze spatial vector data. Binds to 'GDAL'
<doi:10.5281/zenodo.5884351> for reading and writing data, to 'GEOS'
<doi:10.5281/zenodo.11396894> for geometrical operations,
and to 'PROJ' <doi:10.5281/zenodo.5884394> for projection
conversions and datum transformations. Uses by default the 's2'
package for geometry operations on geodetic (long/lat degree)
coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-22 dated 2025-11-10 and 1.0-23 dated 2025-11-28
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 6 ++++++ R/read.R | 4 ++-- R/sf.R | 18 +++++++++++------- inst/doc/sf1.html | 8 ++++---- inst/doc/sf2.html | 6 +++--- inst/doc/sf4.html | 2 +- inst/doc/sf7.html | 10 +++++----- inst/docker/gdal/Dockerfile | 13 ++++++++++++- man/st_read.Rd | 4 ++-- src/gdal_utils.cpp | 2 +- tests/sfc.Rout.save | 12 ++++-------- tests/stars.R | 20 ++++++++++++++++---- tests/stars.Rout.save | 31 ++++++++++++++++++++++--------- 15 files changed, 106 insertions(+), 64 deletions(-)
Title: Read Data Stored in 'DBC' (Compressed 'DBF') Files
Description: Functions for reading and decompressing the 'DBC' (compressed 'DBF') files. Please note that this is the file format used by the Brazilian Ministry of Health ('DATASUS') to publish healthcare datasets. It is not related to the 'FoxPro' or 'CANdb' 'DBC' file formats.
Author: Daniela Petruzalek [aut, cre, cph],
Mark Adler [cph, ctb],
Pablo Marcondes Fonseca [cph, ctb]
Maintainer: Daniela Petruzalek <daniela.petruzalek@gmail.com>
This is a re-admission after prior archival of version 1.0.7 dated 2024-05-08
Diff between read.dbc versions 1.0.7 dated 2024-05-08 and 1.2.0 dated 2025-11-28
DESCRIPTION | 21 +++++---- MD5 | 37 ++++++++++------ NAMESPACE | 2 NEWS.md | 17 +++++++ R/dbc2dbf.R | 22 +++++++-- R/dbf2dbc.R |only R/read.dbc.R | 23 +++++----- README.md | 2 inst/CHANGELOG.md | 19 ++++++++ man/dbc2dbf.Rd | 2 man/dbf2dbc.Rd |only man/read.dbc.Rd | 4 - src/blast.c | 119 ++++++++++++++++++++++++++++------------------------ src/blast.h | 7 +-- src/dbc2dbf.c | 102 ++++++++++++++++++++++++++++++++++---------- src/dbf2dbc.c |only src/implode.c |only src/implode.h |only src/read_dbc_init.c | 20 +++++++- tests |only 20 files changed, 274 insertions(+), 123 deletions(-)
Title: Subset- And Name-Aware Array Utility Functions
Description: Stacking arrays according to dimension names, subset-aware
splitting and mapping of functions, intersecting along arbitrary
dimensions, converting to and from data.frames, and many other helper
functions.
Author: Michael Schubert [aut, cre, cph]
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between narray versions 0.5.1 dated 2022-10-02 and 0.5.2 dated 2025-11-28
narray-0.5.1/narray/R/stack_old.r |only narray-0.5.2/narray/DESCRIPTION | 16 +- narray-0.5.2/narray/MD5 | 13 +- narray-0.5.2/narray/NEWS.md | 5 narray-0.5.2/narray/build/vignette.rds |binary narray-0.5.2/narray/inst/doc/narray.R | 6 - narray-0.5.2/narray/inst/doc/narray.html | 175 +++++++++++++++---------------- narray-0.5.2/narray/src/stack.cpp | 42 +++---- 8 files changed, 124 insertions(+), 133 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd],
sungho Choi [aut],
Mingu Jee [aut],
Wonbin Hahn [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.21 dated 2025-10-24 and 0.5.22 dated 2025-11-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 3 +++ R/jskm.R | 9 +++++++-- R/svyjskm.R | 19 ++++++++++++++----- inst/doc/jskm.html | 4 ++-- man/jskm.Rd | 3 +++ man/svyjskm.Rd | 3 +++ 8 files changed, 43 insertions(+), 20 deletions(-)
Title: Analyse Biological Invasion Costs with the 'InvaCost' Database
Description: Provides an up-to-date version of the 'InvaCost' database
(<doi:10.6084/m9.figshare.12668570>) in R, and
several functions to analyse the costs of invasive alien species
(<doi:10.1111/2041-210X.13929>).
Author: Boris Leroy [cre, aut],
Andrew Kramer [aut],
Anne-Charlotte Vaissiere [ctb],
Christophe Diagne [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between invacost versions 1.1-6 dated 2024-02-11 and 1.1-7 dated 2025-11-28
DESCRIPTION | 28 +++++++++++++++++++++------ MD5 | 6 ++--- R/getInvaCostVersion.R | 50 +++++++++++++++++++++++++++++++------------------ build/partial.rdb |binary 4 files changed, 57 insertions(+), 27 deletions(-)
Title: Algorithms for Routing and Solving the Traffic Assignment
Problem
Description: Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm.
Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>),
bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://www.cs.princeton.edu/courses/archive/spr06/cos423/Handouts/EPP%20shortest%20path%20algorithms.pdf>),
A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>),
new bidirectional A* (Pijls & Post (2009) <https://repub.eur.nl/pub/16100/ei2009-10.pdf>),
Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>),
PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>).
Algorithms for solving the traffic assignment problem are All-or-Nothing assignment,
Method of Successive Averages,
Frank-Wolfe algorithm (M. Fukus [...truncated...]
Author: Vincent Larmet [aut, cre]
Maintainer: Vincent Larmet <larmet.vincent@gmail.com>
Diff between cppRouting versions 3.1 dated 2022-12-01 and 3.2 dated 2025-11-28
DESCRIPTION | 17 - MD5 | 28 +- NEWS.md | 123 +++++---- R/RcppExports.R | 150 ++++++------ build/vignette.rds |binary inst/doc/cppRouting.R | 12 inst/doc/cppRouting.html | 586 ++++++++++++++++++++++++++++++++++------------- src/Makevars | 1 src/Makevars.win | 1 src/distance_mat.cpp | 2 src/distance_pair.cpp | 2 src/graph.h | 2 src/path_mat.cpp | 2 src/path_pair.cpp | 2 src/wrapper.cpp | 28 +- 15 files changed, 612 insertions(+), 344 deletions(-)
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2017-10-20 0.7.6
2016-09-02 0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-04 0.5
2023-07-06 0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-03 3.0
2024-11-05 2.4.1
2023-01-12 2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-24 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-11 2.2.5
2024-01-11 2.2.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-02 0.0.5
2023-11-16 0.0.4
2023-10-17 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-01 0.1.7
2023-11-07 0.1.6
2022-09-02 0.1.5
2022-06-20 0.1.4
2019-05-09 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-07 2.3
2022-09-07 2.2
2022-04-06 2.1
2021-04-02 2.0
2021-02-04 1.7
2021-01-10 1.6
2020-12-16 1.5
2020-11-01 1.4.3
2020-09-01 1.4.2
2020-08-02 1.4.1
2020-06-26 1.4
2020-04-26 1.3.3
2020-03-16 1.3.2
2020-01-23 1.3.1
2019-12-09 1.3
2018-11-06 1.1
2018-04-08 1.0-9
2014-01-14 1.0-8
2011-12-27 1.0-7
2010-10-01 1.0-6
2010-09-21 1.0-5
2009-02-15 1.0-4
2007-07-18 1.0-3
2005-10-20 1.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-05 1.0.1
2022-10-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-27 1.7.5
2023-05-26 1.7.4
2022-02-07 1.7.3
2021-05-13 1.7.2
2021-02-18 1.7.1
2019-09-03 1.7.0
2019-06-20 1.5.0
2019-02-21 1.1.0
2018-10-30 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-25 0.1.1
2023-03-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-19 0.4
2023-01-30 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-28 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-11 0.0.2
2023-04-05 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-13 1.0.0
2022-10-10 0.2.3
2022-06-03 0.2.2
2022-05-17 0.2.1
2021-12-15 0.1.1
2021-12-01 0.1.0
Title: Rearrangement Distances Between Unrooted Phylogenetic Trees
Description: Fast calculation of the Subtree Prune and Regraft (SPR),
Tree Bisection and Reconnection (TBR) and Replug distances between
unrooted trees, using the algorithms of Whidden and
Matsen (2017) <doi:10.48550/arXiv.1511.07529>.
Author: Martin R. Smith [aut, cre, cph] ,
Chris Whidden [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TBRDist versions 1.0.2 dated 2020-09-17 and 1.0.3 dated 2025-11-28
DESCRIPTION | 18 - MD5 | 20 +- NEWS.md | 4 build/vignette.rds |binary inst/CITATION | 10 - inst/doc/TBRDist.R | 2 inst/doc/TBRDist.html | 191 ++++++++++++-------- man/TreeRearrangementDistances.Rd | 348 +++++++++++++++++++------------------- man/dot-PrepareTrees.Rd | 64 +++--- man/internals.Rd | 86 ++++----- src/RcppExports.cpp | 5 11 files changed, 398 insertions(+), 350 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.1.1 dated 2025-10-08 and 5.0.0 dated 2025-11-28
rxode2-4.1.1/rxode2/tests/testthat/433.qs |only rxode2-4.1.1/rxode2/tests/testthat/etTrans-drop.qs |only rxode2-4.1.1/rxode2/tests/testthat/etTrans1.qs |only rxode2-4.1.1/rxode2/tests/testthat/keep-756.qs |only rxode2-4.1.1/rxode2/tests/testthat/lincmt-solve-focei-sol.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-data-setup.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-etTrans-1.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-etTrans-780.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-example-3-1.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-infusion-bolus.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-issue-393.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-issue-398.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-issue-430.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-issue-468.qs |only rxode2-4.1.1/rxode2/tests/testthat/test-nmtest.qs |only rxode2-5.0.0/rxode2/DESCRIPTION | 15 rxode2-5.0.0/rxode2/MD5 | 148 +-- rxode2-5.0.0/rxode2/NAMESPACE | 4 rxode2-5.0.0/rxode2/NEWS.md | 20 rxode2-5.0.0/rxode2/R/asModel.R | 9 rxode2-5.0.0/rxode2/R/mlogit.R | 13 rxode2-5.0.0/rxode2/R/piping.R | 6 rxode2-5.0.0/rxode2/R/rxUiGet.R | 2 rxode2-5.0.0/rxode2/R/rxode2.R | 58 - rxode2-5.0.0/rxode2/R/rxode2_md5.R | 2 rxode2-5.0.0/rxode2/R/rxsolve.R | 2 rxode2-5.0.0/rxode2/R/tran.R | 2 rxode2-5.0.0/rxode2/R/ui-assign-parts.R | 2 rxode2-5.0.0/rxode2/R/ui-getControl.R | 4 rxode2-5.0.0/rxode2/R/ui-rename.R | 4 rxode2-5.0.0/rxode2/R/ui.R | 18 rxode2-5.0.0/rxode2/build/linCmtTest.R | 4 rxode2-5.0.0/rxode2/build/partial.rdb |binary rxode2-5.0.0/rxode2/build/vignette.rds |binary rxode2-5.0.0/rxode2/inst/doc/rxode2-syntax.html | 26 rxode2-5.0.0/rxode2/inst/include/rxode2_model_shared.c | 66 + rxode2-5.0.0/rxode2/inst/include/rxode2parseStruct.h | 1 rxode2-5.0.0/rxode2/inst/include/rxode2parseVer.h | 4 rxode2-5.0.0/rxode2/inst/include/rxode2parse_control.h | 3 rxode2-5.0.0/rxode2/man/as.model.Rd | 4 rxode2-5.0.0/rxode2/man/mexpit.Rd | 9 rxode2-5.0.0/rxode2/man/rxLastCompile.Rd |only rxode2-5.0.0/rxode2/man/stat_amt.Rd | 6 rxode2-5.0.0/rxode2/man/stat_cens.Rd | 6 rxode2-5.0.0/rxode2/src/codegen2.h | 66 + rxode2-5.0.0/rxode2/src/etTran.cpp | 343 +++++-- rxode2-5.0.0/rxode2/src/genModelVars.c | 1 rxode2-5.0.0/rxode2/src/genModelVars.h | 6 rxode2-5.0.0/rxode2/src/init.c | 2 rxode2-5.0.0/rxode2/src/mlogit.c | 26 rxode2-5.0.0/rxode2/src/par_solve.h | 6 rxode2-5.0.0/rxode2/src/print_node.h | 2 rxode2-5.0.0/rxode2/src/qs.cpp | 10 rxode2-5.0.0/rxode2/src/rxData.cpp | 176 +-- rxode2-5.0.0/rxode2/tests/testthat/433.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/etTrans-drop.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/etTrans1.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/keep-756.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/lincmt-solve-focei-sol.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-alag.R | 6 rxode2-5.0.0/rxode2/tests/testthat/test-cbind-study-individual.R | 6 rxode2-5.0.0/rxode2/tests/testthat/test-convertId.R | 3 rxode2-5.0.0/rxode2/tests/testthat/test-data-setup.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-data-table.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-etTrans-1.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-etTrans-780.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-etTrans.R | 14 rxode2-5.0.0/rxode2/tests/testthat/test-example-3-1.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-example-3-1.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-infusion-bolus.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-infusion-bolus.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-issue-393.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-issue-398.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-issue-430.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-issue-468.qs2 |only rxode2-5.0.0/rxode2/tests/testthat/test-keep.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-lincmt-solve.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-mix.R | 112 ++ rxode2-5.0.0/rxode2/tests/testthat/test-mlogit.R | 14 rxode2-5.0.0/rxode2/tests/testthat/test-nmtest.R | 6 rxode2-5.0.0/rxode2/tests/testthat/test-nodup-keep.R | 2 rxode2-5.0.0/rxode2/tests/testthat/test-par-solve.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-rxIs.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-rxode-issue-393.R | 28 rxode2-5.0.0/rxode2/tests/testthat/test-rxode-issue-398.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-rxode-issue-430.R | 14 rxode2-5.0.0/rxode2/tests/testthat/test-rxode-issue-433.R | 4 rxode2-5.0.0/rxode2/tests/testthat/test-rxode-issue-468.R | 2 rxode2-5.0.0/rxode2/tests/testthat/test-ui-piping.R | 133 +- rxode2-5.0.0/rxode2/tests/testthat/test-zzzz-plot.R | 465 +++++++--- 90 files changed, 1304 insertions(+), 613 deletions(-)
Title: The Flexible Spatial Scan Statistic
Description: Provides functions for detecting spatial clusters using the flexible
spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
This package implements a wrapper for the 'C' routine used in the 'FleXScan' 3.1.2
<https://sites.google.com/site/flexscansoftware/home> developed by Takahashi,
Yokoyama, and Tango. For details, see Otani et al. (2021) <doi:10.18637/jss.v099.i13>.
Author: Takahiro Otani [aut, cre],
Kunihiko Takahashi [aut]
Maintainer: Takahiro Otani <t.otani@aichi-cc.jp>
This is a re-admission after prior archival of version 1.1.0 dated 2023-03-01
Diff between rflexscan versions 1.1.0 dated 2023-03-01 and 1.2.0 dated 2025-11-28
DESCRIPTION | 29 +++++++++++++++--------- MD5 | 30 ++++++++++++------------- NEWS.md | 7 +++++ R/RcppExports.R | 3 ++ R/flexscan.R | 48 +++++++++++++++++++++++++++++++++++------ inst/CITATION | 34 ++++++++++++++--------------- man/choropleth.Rd | 6 ++++- man/plot.rflexscan.Rd | 6 ++++- man/print.rflexscan.Rd | 4 +++ man/print.rflexscanCluster.Rd | 5 ++++ man/print.summary.rflexscan.Rd | 5 ++++ man/rflexscan-package.Rd | 9 +++++++ man/rflexscan.Rd | 5 +++- man/runFleXScan.Rd | 3 ++ man/summary.rflexscan.Rd | 5 ++++ src/flscan312.cpp | 38 ++++++++++++++++++++++++++++---- 16 files changed, 178 insertions(+), 59 deletions(-)
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.1.1 dated 2025-09-12 and 1.1.2 dated 2025-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 1 - R/utility_functions.R | 2 +- 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Design and Analysis for Factorial Experiments
Description: Provides design-based and model-based estimators for the population average marginal component effects in general factorial experiments, including conjoint analysis. The package also implements a series of recommendations offered in de la Cuesta, Egami, and Imai (2022) <doi:10.1017/pan.2020.40>, and Egami and Imai (2019) <doi:10.1080/01621459.2018.1476246>.
Author: Naoki Egami [aut, cre],
Brandon de la Cuesta [aut],
Kosuke Imai [aut]
Maintainer: Naoki Egami <naoki.egami5@gmail.com>
This is a re-admission after prior archival of version 1.0.1 dated 2020-05-11
Diff between factorEx versions 1.0.1 dated 2020-05-11 and 1.1.0 dated 2025-11-28
factorEx-1.0.1/factorEx/R/factorEx-package.R |only factorEx-1.0.1/factorEx/man/factorEx-package.Rd |only factorEx-1.1.0/factorEx/DESCRIPTION | 25 ++++++++++++--- factorEx-1.1.0/factorEx/MD5 | 38 +++++++++++------------- factorEx-1.1.0/factorEx/R/AME_fit_basic.R | 2 - factorEx-1.1.0/factorEx/R/decompose_pAMCE.R | 1 factorEx-1.1.0/factorEx/R/design_pAMCE.R | 6 +-- factorEx-1.1.0/factorEx/R/diagnose_pAMCE.R | 2 + factorEx-1.1.0/factorEx/R/model_pAMCE.R | 26 +++++++--------- factorEx-1.1.0/factorEx/R/plot_pAMCE.R | 1 factorEx-1.1.0/factorEx/R/summary_pAMCE.R | 1 factorEx-1.1.0/factorEx/R/weights_pAMCE.R | 7 ++-- factorEx-1.1.0/factorEx/man/OnoBurden.Rd | 4 +- factorEx-1.1.0/factorEx/man/design_pAMCE.Rd | 6 +-- factorEx-1.1.0/factorEx/man/diagnose_pAMCE.Rd | 3 + factorEx-1.1.0/factorEx/man/model_pAMCE.Rd | 24 ++++++--------- factorEx-1.1.0/factorEx/man/plot.pAMCE.Rd | 3 + factorEx-1.1.0/factorEx/man/plot_decompose.Rd | 3 + factorEx-1.1.0/factorEx/man/plot_diagnose.Rd | 3 + factorEx-1.1.0/factorEx/man/summary.pAMCE.Rd | 3 + factorEx-1.1.0/factorEx/man/weights_pAMCE.Rd | 3 + 21 files changed, 97 insertions(+), 64 deletions(-)
Title: Ecological Limit Function Model Generation and Analysis Toolkit
Description: A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the 'elfgen' framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
Author: Joseph Kleiner [aut] ,
Robert Burgholzer [ctb] ,
Connor Brogan [cre]
Maintainer: Connor Brogan <connor.brogan@deq.virginia.gov>
This is a re-admission after prior archival of version 2.3.3 dated 2022-08-23
Diff between elfgen versions 2.3.3 dated 2022-08-23 and 2.3.4 dated 2025-11-28
DESCRIPTION | 35 +++++-- MD5 | 33 +++--- NEWS.md |only R/bkpt-pwit.R | 3 R/bkpt-ymax.R | 3 R/elfchange.R | 3 R/elfdata.R | 192 +++++++++++++++++++++++++--------------- R/elfgen.R | 27 ++++- R/richness-change.R | 3 README.md | 6 - man/bkpt_pwit.Rd | 3 man/bkpt_ymax.Rd | 3 man/elfchange.Rd | 3 man/elfdata.Rd | 33 +++++- man/elfgen.Rd | 14 ++ man/richness_change.Rd | 3 tests/testthat/test-elfchange.R | 16 +-- tests/testthat/test-elfdata.R | 10 +- 18 files changed, 259 insertions(+), 131 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-15 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-12 1.23.0
2023-08-30 1.22.6
2022-12-02 1.22.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-23 0.1.5.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-13 1.0.1
2018-08-31 1.0
Title: Inferring Latent Diffusion Networks
Description: This is an R implementation of the netinf algorithm (Gomez Rodriguez, Leskovec, and Krause, 2010)<doi:10.1145/1835804.1835933>. Given a set of events that spread between a set of nodes the algorithm infers the most likely stable diffusion network that is underlying the diffusion process.
Author: Fridolin Linder [aut, cre],
Bruce Desmarais [ctb]
Maintainer: Fridolin Linder <fridolin.linder@gmail.com>
Diff between NetworkInference versions 1.2.4 dated 2019-02-28 and 1.2.5 dated 2025-11-28
NetworkInference-1.2.4/NetworkInference/vignettes/readme.html |only NetworkInference-1.2.5/NetworkInference/DESCRIPTION | 9 NetworkInference-1.2.5/NetworkInference/MD5 | 22 NetworkInference-1.2.5/NetworkInference/NEWS.md | 13 NetworkInference-1.2.5/NetworkInference/R/zzz.R | 2 NetworkInference-1.2.5/NetworkInference/build/partial.rdb |only NetworkInference-1.2.5/NetworkInference/build/vignette.rds |binary NetworkInference-1.2.5/NetworkInference/inst/CITATION | 82 - NetworkInference-1.2.5/NetworkInference/inst/doc/quickstart_vignette.R | 20 NetworkInference-1.2.5/NetworkInference/inst/doc/quickstart_vignette.html | 271 ++- NetworkInference-1.2.5/NetworkInference/inst/doc/tutorial_vignette.R | 86 - NetworkInference-1.2.5/NetworkInference/inst/doc/tutorial_vignette.html | 727 ++++++---- NetworkInference-1.2.5/NetworkInference/man/policies.Rd | 2 13 files changed, 737 insertions(+), 497 deletions(-)
More information about NetworkInference at CRAN
Permanent link
Title: Zero-Truncated Poisson Lognormal Distribution
Description: Functions for obtaining the density, random variates
and maximum likelihood estimates of the Zero-truncated Poisson lognormal
distribution and their mixture distribution.
Author: Masatoshi Katabuchi [aut, cre, cph]
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>
Diff between ztpln versions 0.1.2 dated 2021-10-09 and 0.1.3 dated 2025-11-28
ztpln-0.1.2/ztpln/R/dztpln.r |only ztpln-0.1.2/ztpln/R/dztplnm.r |only ztpln-0.1.2/ztpln/R/ztpln.r |only ztpln-0.1.2/ztpln/R/ztplnMLE.r |only ztpln-0.1.2/ztpln/R/ztplnmMLE.r |only ztpln-0.1.2/ztpln/inst/doc/ztpln.rmd |only ztpln-0.1.2/ztpln/tests/testthat/test_ztpln.r |only ztpln-0.1.2/ztpln/vignettes/ztpln.rmd |only ztpln-0.1.3/ztpln/DESCRIPTION | 20 ztpln-0.1.3/ztpln/MD5 | 38 - ztpln-0.1.3/ztpln/R/dztpln.R |only ztpln-0.1.3/ztpln/R/dztplnm.R |only ztpln-0.1.3/ztpln/R/ztpln.R |only ztpln-0.1.3/ztpln/R/ztplnMLE.R |only ztpln-0.1.3/ztpln/R/ztplnmMLE.R |only ztpln-0.1.3/ztpln/build/vignette.rds |binary ztpln-0.1.3/ztpln/inst/doc/ztpln.R | 10 ztpln-0.1.3/ztpln/inst/doc/ztpln.Rmd |only ztpln-0.1.3/ztpln/inst/doc/ztpln.html | 562 +++++++++++++++++++------- ztpln-0.1.3/ztpln/man/dztpln.Rd | 2 ztpln-0.1.3/ztpln/man/dztplnm.Rd | 2 ztpln-0.1.3/ztpln/man/ztpln-package.Rd | 2 ztpln-0.1.3/ztpln/man/ztplnMLE.Rd | 2 ztpln-0.1.3/ztpln/man/ztplnmMLE.Rd | 2 ztpln-0.1.3/ztpln/src/Makevars | 2 ztpln-0.1.3/ztpln/src/Makevars.win | 2 ztpln-0.1.3/ztpln/tests/testthat/test_ztpln.R |only ztpln-0.1.3/ztpln/vignettes/ztpln.Rmd |only 28 files changed, 454 insertions(+), 190 deletions(-)
Title: Access Indonesian Data via Public APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'Nager.Date', 'World Bank API', and 'REST Countries API', retrieving real-time or historical
data related to Indonesia, such as holidays, economic indicators, and international
demographic and geopolitical indicators. The package also includes a curated collection of
open datasets focused on Indonesia, covering topics such as consumer prices, poverty
probability, food prices by region, tourism destinations, and minimum wage statistics.
The package supports reproducible research and teaching by integrating reliable
international APIs and structured datasets from public, academic, and government sources.
For more information on the APIs, see:
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
and 'REST Countries API' <https://restcountries.com/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between IndonesiAPIs versions 0.1.0 dated 2025-09-09 and 0.1.1 dated 2025-11-28
DESCRIPTION | 9 - MD5 | 101 +++++++++--------- NAMESPACE | 2 NEWS.md |only R/data-documentation.R | 2 R/get_country_info_idn.R | 56 +++++++++- R/get_indonesia_child_mortality.R | 50 +++++++-- R/get_indonesia_cpi.R | 50 +++++++-- R/get_indonesia_energy_use.R | 50 +++++++-- R/get_indonesia_gdp.R | 50 +++++++-- R/get_indonesia_holidays.R | 47 +++++++- R/get_indonesia_hospital_beds.R | 50 +++++++-- R/get_indonesia_life_expectancy.R | 50 +++++++-- R/get_indonesia_literacy_rate.R | 73 +++++++++---- R/get_indonesia_population.R | 77 ++++++++++---- R/get_indonesia_unemployment.R | 84 +++++++++++---- R/indonesiapis-package.R | 2 R/utils.R | 2 R/view_datasets_IndonesiAPIs.R | 2 README.md | 6 + build/vignette.rds |binary inst/CITATION | 7 - inst/doc/IndonesiAPIs_vignette.html | 5 man/get_country_info_idn.Rd | 3 man/get_indonesia_child_mortality.Rd | 5 man/get_indonesia_cpi.Rd | 5 man/get_indonesia_energy_use.Rd | 5 man/get_indonesia_gdp.Rd | 5 man/get_indonesia_holidays.Rd | 3 man/get_indonesia_hospital_beds.Rd | 5 man/get_indonesia_life_expectancy.Rd | 5 man/get_indonesia_literacy_rate.Rd | 23 ++-- man/get_indonesia_population.Rd | 27 ++--- man/get_indonesia_unemployment.Rd | 26 ++-- tests/testthat/test-Bali_tbl_df.R | 2 tests/testthat/test-DKIJakarta_tbl_df.R | 2 tests/testthat/test-SumateraUtara_tbl_df.R | 2 tests/testthat/test-bali_tourism_tbl_df.R | 2 tests/testthat/test-get_country_info_idn.R | 6 - tests/testthat/test-get_indonesia_child_mortality.R | 7 - tests/testthat/test-get_indonesia_cpi.R | 18 ++- tests/testthat/test-get_indonesia_energy_use.R | 33 ++---- tests/testthat/test-get_indonesia_gdp.R | 75 ++++++-------- tests/testthat/test-get_indonesia_holidays.R | 69 +++++++++--- tests/testthat/test-get_indonesia_hospital_beds.R | 72 +++++++++---- tests/testthat/test-get_indonesia_life_expectancy.R | 87 +++++----------- tests/testthat/test-get_indonesia_literacy_rate.R | 99 ++++++++---------- tests/testthat/test-get_indonesia_population.R | 102 +++++++------------ tests/testthat/test-get_indonesia_unemployment.R | 107 ++++++++------------ tests/testthat/test-indonesia_latlong_df.R | 2 tests/testthat/test-indonesia_minwage_tbl_df.R | 2 tests/testthat/test-view_datasets_IndonesiAPIs.R | 2 52 files changed, 985 insertions(+), 591 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Roger Bivand [ctb] ,
Andrew Brown [ctb] ,
Michael Chirico [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-80 dated 2025-11-05 and 1.8-86 dated 2025-11-28
DESCRIPTION | 12 ++-- MD5 | 97 +++++++++++++++++---------------- NAMESPACE | 2 NEWS.md | 30 ++++++++++ R/Agenerics.R | 1 R/SpatRasterDataset.R | 13 +++- R/chunk.R |only R/click.R | 6 +- R/extent.R | 10 +++ R/focal.R | 10 ++- R/generics.R | 81 +++++++++++++++++++--------- R/geom.R | 9 ++- R/messages.R | 6 +- R/plot.R | 1 R/plot_add.R | 10 +-- R/plot_raster.R | 3 + R/plot_vector.R | 33 +++++++---- R/spatvec.R | 28 +++++++++ R/vect.R | 44 +++++++++++++-- R/xyRowColCell.R | 34 +++++------ inst/tinytest/test_crds.R | 7 ++ inst/tinytest/test_extract.R | 2 inst/tinytest/test_vector-empty.R |only man/boundaries.Rd | 13 ++-- man/centroids.Rd | 12 +++- man/chunk.Rd |only man/ext.Rd | 1 man/extract.Rd | 6 +- man/extractRange.Rd | 2 man/fill.Rd | 25 +++++++- man/is.valid.Rd | 11 +++ man/legend.Rd | 3 - man/makeTiles.Rd | 2 man/plot.Rd | 2 man/resample.Rd | 2 man/stretch.Rd | 6 +- man/vect.Rd | 4 - src/Makevars.ucrt | 14 ++-- src/RcppModule.cpp | 2 src/distRaster.cpp | 100 ++++++++++++++++++++++++---------- src/distValueRaster.cpp | 8 +- src/gdal_multidimensional.cpp | 2 src/geos_methods.cpp | 21 ++++--- src/nearest.cpp | 8 +- src/raster_methods.cpp | 109 ++++++++++++++++++++++++++++++++------ src/read_gdal.cpp | 17 ++++- src/read_ogr.cpp | 5 + src/spatRaster.cpp | 40 +++++++------ src/spatRaster.h | 6 +- src/vecmath.h | 15 ++++- src/write_ogr.cpp | 37 ++++++++---- 51 files changed, 649 insertions(+), 263 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] ,
Zachary Foster [ctb] ,
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.3.0 dated 2024-07-03 and 0.3.5 dated 2025-11-28
DESCRIPTION | 25 +++--- MD5 | 54 ++++++++------ NAMESPACE | 7 + NEWS.md | 26 +++++++ R/accepted_name.R | 5 - R/backup_object.R | 12 +-- R/id_generator.R | 10 +- R/imports.R | 1 R/indented_list.R | 6 + R/internal.R | 158 +++++++++++++++++++++++++++++++++++++++++++ R/merge_taxa.R | 5 - R/print_name.R | 2 R/reindex.R |only R/sort_taxa.R |only R/summary.R | 36 +++++++-- R/sysdata.rda |binary R/tax2traits.R | 49 ------------- R/taxlist2df.R | 7 + R/tv2taxlist.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/Easplist.rda |binary inst/doc/taxlist-intro.R | 8 +- inst/doc/taxlist-intro.html | 71 ++++++++++--------- man/arrange_taxa.Rd |only man/figures/genera_bar-1.png |binary man/print_name.Rd | 3 man/reindex.Rd |only man/sort_taxa.Rd |only man/tv.home.Rd |only man/tv2taxlist.Rd | 2 31 files changed, 337 insertions(+), 152 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.4-2 dated 2025-09-28 and 3.5-0 dated 2025-11-28
DESCRIPTION | 16 - MD5 | 91 ++++----- NAMESPACE | 17 + NEWS | 75 +++++++ R/aaaa.R | 2 R/augment.msr.R | 10 - R/bermantest.R | 2 R/diagnoseppm.R | 305 ++++++++++++++++---------------- R/dppm.R | 8 R/eem.R | 15 + R/evidence.R | 4 R/evidenceslrm.R | 12 - R/kppm.R | 2 R/measures.R | 49 ++++- R/mpl.R | 2 R/mppm.R | 78 ++++++-- R/parres.R | 233 ++++++++++++++++++------ R/predictmppm.R | 74 +++++++ R/qqplotppm.R | 11 - R/quadratmtest.R | 4 R/quadrattest.R | 2 R/resid4plot.R | 35 +-- R/residexactppm.R |only R/residuals.mppm.R | 5 R/rocmodel.R | 389 ++++++++++++++++++++++++++++++++++++++--- R/slrm.R | 276 ++++++++++++++++++++++------- R/subfits.R | 39 +++- R/summary.mppm.R | 11 - R/sysdata.rda |binary R/update.ppm.R | 8 build/partial.rdb |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/auc.ppm.Rd | 4 man/diagnose.ppm.Rd | 21 +- man/fitted.slrm.Rd | 44 +++- man/lurking.Rd | 2 man/macros/defns.Rd | 3 man/mppm.Rd | 22 ++ man/parres.Rd | 29 ++- man/predict.slrm.Rd | 36 +++ man/qqplot.ppm.Rd | 18 - man/residualMeasure.Rd | 6 man/roc.ppm.Rd | 51 ++++- man/slrm.Rd | 90 ++++++++- man/spatstat.model-internal.Rd | 24 +- tests/testsR1.R | 7 47 files changed, 1611 insertions(+), 525 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Memory-Map Character Files
Description: Uses memory-mapping to enable the random access of elements of
a text file of characters separated by characters as if it were a simple
R(cpp) matrix.
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between mmapcharr versions 0.3.0 dated 2019-02-26 and 0.3.1 dated 2025-11-28
mmapcharr-0.3.0/mmapcharr/man/mmapcharr.Rd |only mmapcharr-0.3.1/mmapcharr/DESCRIPTION | 13 mmapcharr-0.3.1/mmapcharr/MD5 | 44 +- mmapcharr-0.3.1/mmapcharr/NAMESPACE | 26 - mmapcharr-0.3.1/mmapcharr/R/RcppExports.R | 38 - mmapcharr-0.3.1/mmapcharr/R/extract.R | 166 ++++---- mmapcharr-0.3.1/mmapcharr/R/file-dim.R | 162 ++++---- mmapcharr-0.3.1/mmapcharr/R/mmapchar.R | 268 ++++++------- mmapcharr-0.3.1/mmapcharr/R/mmapcharr-package.r | 15 mmapcharr-0.3.1/mmapcharr/R/utils.R | 40 +- mmapcharr-0.3.1/mmapcharr/inst/testdata/geno3pops.lfmm | 300 +++++++-------- mmapcharr-0.3.1/mmapcharr/inst/testdata/test-windows.txt | 4 mmapcharr-0.3.1/mmapcharr/man/Extract.Rd | 70 +-- mmapcharr-0.3.1/mmapcharr/man/dim_file.Rd | 46 +- mmapcharr-0.3.1/mmapcharr/man/mmapchar-class.Rd | 62 +-- mmapcharr-0.3.1/mmapcharr/man/mmapchar-methods.Rd | 79 +-- mmapcharr-0.3.1/mmapcharr/man/mmapcharr-package.Rd |only mmapcharr-0.3.1/mmapcharr/man/nelem.Rd | 44 +- mmapcharr-0.3.1/mmapcharr/man/nline.Rd | 44 +- mmapcharr-0.3.1/mmapcharr/src/Makevars | 1 mmapcharr-0.3.1/mmapcharr/src/RcppExports.cpp | 5 mmapcharr-0.3.1/mmapcharr/tests/testthat.R | 8 mmapcharr-0.3.1/mmapcharr/tests/testthat/test-extract.R | 132 +++--- mmapcharr-0.3.1/mmapcharr/tests/testthat/test-file-dim.R | 84 ++-- 24 files changed, 825 insertions(+), 826 deletions(-)
Title: Bindings for 'Mapbox' Ear Cutting Triangulation Library
Description: Provides constrained triangulation of polygons. Ear cutting (or
ear clipping) applies constrained triangulation by successively 'cutting'
triangles from a polygon defined by path/s. Holes are supported by introducing
a bridge segment between polygon paths. This package wraps the 'header-only'
library 'earcut.hpp' <https://github.com/mapbox/earcut.hpp> which includes
a reference to the method used by Held, M. (2001) <doi:10.1007/s00453-001-0028-4>.
Author: Michael Sumner [aut, cre],
Andrew Smith [ctb] ,
Mapbox [cph] ,
Mark Padgham [ctb] ,
David Cooley [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between decido versions 0.3.0 dated 2020-05-19 and 0.4.0 dated 2025-11-28
decido-0.3.0/decido/tests/testthat/Rplots.pdf |only decido-0.4.0/decido/DESCRIPTION | 16 decido-0.4.0/decido/MD5 | 31 - decido-0.4.0/decido/NEWS.md | 10 decido-0.4.0/decido/R/decido-package.R | 7 decido-0.4.0/decido/README.md | 18 decido-0.4.0/decido/build/vignette.rds |binary decido-0.4.0/decido/inst/doc/decido.R | 36 - decido-0.4.0/decido/inst/doc/decido.Rmd | 22 decido-0.4.0/decido/inst/doc/decido.html | 547 ++++++++------------ decido-0.4.0/decido/inst/include/earcut.h | 2 decido-0.4.0/decido/man/decido-package.Rd | 14 decido-0.4.0/decido/man/figures/README-tricks-1.png |binary decido-0.4.0/decido/src/Makevars | 1 decido-0.4.0/decido/src/Makevars.win | 1 decido-0.4.0/decido/src/RcppExports.cpp | 5 decido-0.4.0/decido/vignettes/decido.Rmd | 22 17 files changed, 315 insertions(+), 417 deletions(-)
Title: Removal of Unwanted Technical Variation from UK Biobank NMR
Metabolomics Biomarker Data
Description: A suite of utilities for working with the UK Biobank
<https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance spectroscopy (NMR)
metabolomics data <https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>.
Includes functions for extracting biomarkers from decoded UK Biobank field
data, removing unwanted technical variation from biomarker concentrations,
computing an extended set of lipid, fatty acid, and cholesterol fractions,
and for re-deriving composite biomarkers and ratios after adjusting data
for unwanted biological variation. For further details on methods see
Ritchie SC et al. Sci Data (2023) <doi:10.1038/s41597-023-01949-y>.
Author: Scott C Ritchie [aut, cre]
Maintainer: Scott C Ritchie <sritchie73@gmail.com>
Diff between ukbnmr versions 3.2.0 dated 2024-11-14 and 3.3.0 dated 2025-11-27
DESCRIPTION | 11 +- MD5 | 14 +-- NEWS.md | 17 +++ R/biomarker_qc.R | 13 +++ R/utils.R | 2 build/vignette.rds |binary inst/doc/ukbnmr.R | 218 +++++++++++++++++++++++++-------------------------- inst/doc/ukbnmr.html | 5 - 8 files changed, 156 insertions(+), 124 deletions(-)
Title: Tools of Utilization and Cost in Healthcare
Description: R implementation of the software tools developed in the H-CUP
(Healthcare Cost and Utilization Project) <https://hcup-us.ahrq.gov>
and AHRQ (Agency for Healthcare Research and Quality)
<https://www.ahrq.gov>. It currently contains functions for mapping ICD-9
codes to the AHRQ comorbidity measures and translating ICD-9
(resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General
Equivalence Mappings) from CMS (Centers for Medicare and Medicaid
Services).
Author: Wenjie Wang [aut, cre] ,
Yan Li [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between touch versions 0.1-6 dated 2022-07-08 and 0.1-7 dated 2025-11-27
DESCRIPTION | 13 ++++++------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 15 +++++++++++++++ R/cmbd.R | 2 +- R/crosswalk.R | 14 +------------- R/data.R | 2 +- R/format.R | 2 +- R/sysdata.rda |binary R/utils.R | 2 +- R/zzz.R | 2 +- README.md | 5 ++--- data/dxDat.rda |binary inst/CITATION | 27 ++++++++++++--------------- man/icd_map.Rd | 12 ------------ src/Makevars | 2 +- src/apply_gems.cpp | 2 +- src/initialize_gems.cpp | 2 +- 17 files changed, 60 insertions(+), 74 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Christophe Dutang [ctb] ,
Reinhold Kainhofer [ctb] ,
Kevin J Owens [ctb],
Ernesto Schirmacher [ctb],
Gian Paolo Clemente [ctb] ,
Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.4.3 dated 2025-09-18 and 1.4.4 dated 2025-11-27
DESCRIPTION | 6 MD5 | 70 + NEWS.md | 465 ++++++------- R/4_financialFunctions.R | 87 +- R/RcppExports.R | 4 build/vignette.rds |binary data/AF92Lt.rda |binary data/AM92Lt.rda |binary data/SoAISTdata.rda |binary data/de_angelis_di_falco.rda |binary data/demoCanada.rda |binary data/demoChina.rda |binary data/demoFrance.rda |binary data/demoGermany.rda |binary data/demoIta.rda |binary data/demoJapan.rda |binary data/demoUk.rda |binary data/demoUsa.rda |binary data/soa08.rda |binary data/soa08Act.rda |binary data/soaLt.rda |binary inst/doc/PensionPlanVal.html | 2 inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 19 inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary inst/doc/compute-detail.html | 2 inst/doc/mortality_projection.Rnw | 2 inst/doc/mortality_projection.pdf |binary inst/doc/pensionfunding.Rmd | 10 inst/doc/pensionfunding.html | 102 +- man/presentValue.Rd | 95 +- src/RcppExports.cpp | 16 src/lifecontingenciesRcpp.cpp | 22 tests/testthat/test-presentValue.R |only tests/testthat/testPresentValue.R |only vignettes/an_introduction_to_lifecontingencies_package.Rnw | 19 vignettes/mortality_projection.Rnw | 2 vignettes/pensionfunding.Rmd | 10 37 files changed, 490 insertions(+), 443 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures. [...truncated...]
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.5.0 dated 2025-10-16 and 0.5.1 dated 2025-11-27
DESCRIPTION | 12 MD5 | 59 +- NAMESPACE | 2 R/Spower.R | 3 R/SpowerBatch.R | 48 + R/p_2r.R | 120 ++-- R/p_mcnemar.test.R | 18 R/p_slr.R |only R/p_t.test.R | 10 R/p_wilcox.test.R | 15 README.md | 70 +- inst/doc/SpowerIntro.Rmd | 52 +- inst/doc/SpowerIntro.html | 82 +-- inst/doc/SpowerIntro_logicals.Rmd | 34 - inst/doc/SpowerIntro_logicals.html | 46 - inst/doc/Spower_TypeSM.html | 14 inst/doc/gpower_examples.Rmd | 873 ++++++++++++++++++++++++++-------- inst/doc/gpower_examples.html | 946 +++++++++++++++++++++++++------------ inst/intro.rds |binary inst/intro2.rds |binary inst/intro3.rds |binary man/Spower.Rd | 48 + man/p_2r.Rd | 93 +-- man/p_mcnemar.test.Rd | 14 man/p_slr.Rd |only man/p_t.test.Rd | 6 man/p_wilcox.test.Rd | 11 tests/testthat/test-Spower.R | 47 - vignettes/SpowerIntro.Rmd | 52 +- vignettes/SpowerIntro_logicals.Rmd | 34 - vignettes/gpower_examples.Rmd | 873 ++++++++++++++++++++++++++-------- vignettes/tetrachoric.png |only 32 files changed, 2516 insertions(+), 1066 deletions(-)
Title: Text Tokenization using Byte Pair Encoding and Unigram Modelling
Description: Unsupervised text tokenizer allowing to perform byte pair encoding and unigram modelling.
Wraps the 'sentencepiece' library <https://github.com/google/sentencepiece> which provides a language independent tokenizer to split text in words and smaller subword units.
The techniques are explained in the paper "SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing" by Taku Kudo and John Richardson (2018) <doi:10.18653/v1/D18-2012>.
Provides as well straightforward access to pretrained byte pair encoding models and subword embeddings trained on Wikipedia using 'word2vec',
as described in "BPEmb: Tokenization-free Pre-trained Subword Embeddings in 275 Languages" by Benjamin Heinzerling and Michael Strube (2018) <http://www.lrec-conf.org/proceedings/lrec2018/pdf/1049.pdf>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Google Inc. [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Google Inc. [ctb, cph] ),
Kenton Varda [ctb, cph] ),
Sanjay Ghemawat [ctb, cph] ),
Jeff Dean [ctb, cph] ),
Laszlo Csomor [ctb, cph] ),
Wink Sav [...truncated...]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between sentencepiece versions 0.2.3 dated 2022-11-13 and 0.2.4 dated 2025-11-27
DESCRIPTION | 6 - MD5 | 8 +- NEWS.md | 5 + src/Makevars | 1 src/third_party/protobuf-lite/google/protobuf/repeated_field.h | 36 +++++++--- 5 files changed, 40 insertions(+), 16 deletions(-)
Title: Detect Line Segments in Images
Description: An implementation of the Line Segment Detector on digital images described in the paper: "LSD: A Fast Line Segment Detector with a False Detection Control" by Rafael Grompone von Gioi et al (2012).
The algorithm is explained at <doi:10.5201/ipol.2012.gjmr-lsd>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Rafael Grompone von Gioi [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between image.LineSegmentDetector versions 0.1.0 dated 2020-07-27 and 0.1.1 dated 2025-11-27
image.LineSegmentDetector-0.1.0/image.LineSegmentDetector/inst/CITATION |only image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/DESCRIPTION | 8 ++--- image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/MD5 | 15 +++++----- image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/NEWS |only image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/R/line_segment_detector.R | 12 ++++---- image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/R/pkg.R | 2 - image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/build |only image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/man/image.LineSegmentDetector-package.Rd | 13 ++++++++ image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/man/image_line_segment_detector.Rd | 12 ++++---- image.LineSegmentDetector-0.1.1/image.LineSegmentDetector/src/RcppExports.cpp | 5 +++ 10 files changed, 42 insertions(+), 25 deletions(-)
More information about image.LineSegmentDetector at CRAN
Permanent link
Title: Implementation of the Unsupervised Smooth Contour Line Detection
for Images
Description: An implementation of the Unsupervised Smooth Contour Detection algorithm for digital images as described in the paper: "Unsupervised Smooth Contour Detection" by Rafael Grompone von Gioi, and Gregory Randall (2016).
The algorithm is explained at <doi:10.5201/ipol.2016.175>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Rafael Grompone von Gioi [ctb, cph] ,
Gregory Randall [ctb, cph] ,
Niccolo Marchi [ctb]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between image.ContourDetector versions 0.1.1 dated 2021-11-17 and 0.1.2 dated 2025-11-27
image.ContourDetector-0.1.1/image.ContourDetector/inst/CITATION |only image.ContourDetector-0.1.2/image.ContourDetector/DESCRIPTION | 8 +++--- image.ContourDetector-0.1.2/image.ContourDetector/MD5 | 13 ++++------ image.ContourDetector-0.1.2/image.ContourDetector/NEWS.md | 5 +++ image.ContourDetector-0.1.2/image.ContourDetector/R/contour_detector.R | 6 ++-- image.ContourDetector-0.1.2/image.ContourDetector/build/partial.rdb |binary image.ContourDetector-0.1.2/image.ContourDetector/man/image.ContourDetector-package.Rd | 13 ++++++++++ image.ContourDetector-0.1.2/image.ContourDetector/man/image_contour_detector.Rd | 6 ++-- 8 files changed, 34 insertions(+), 17 deletions(-)
More information about image.ContourDetector at CRAN
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Title: Read and Write WAV Files
Description: Efficiently read and write Waveform (WAV) audio files <https://en.wikipedia.org/wiki/WAV>.
Support for unsigned 8 bit Pulse-code modulation (PCM), signed 12, 16, 24 and 32 bit
PCM and other encodings.
Author: Daniel Falbel [aut, cre, cph],
Posit, PBC [cph],
David Reid [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between wav versions 0.1.0 dated 2022-11-28 and 0.1.1 dated 2025-11-27
DESCRIPTION | 7 +++---- MD5 | 5 +++-- NEWS.md |only README.md | 1 + 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models with the possibility of non-informative random right or left censoring.
Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value and standard normal distributions as important special cases. Inference is based on likelihood, penalized likelihood and bootstrap methods.
Lastly, some numerical and graphical devices for diagnostic of the fitted models are offered.
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph] ,
Gilberto Paula [aut],
Luis Vanegas [aut]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.2.2 dated 2022-09-03 and 0.2.3 dated 2025-11-27
sglg-0.2.2/sglg/man/influence.sglg.Rd |only sglg-0.2.2/sglg/man/quantile_residuals.Rd |only sglg-0.2.3/sglg/DESCRIPTION | 21 +- sglg-0.2.3/sglg/MD5 | 68 +++++--- sglg-0.2.3/sglg/NAMESPACE | 9 - sglg-0.2.3/sglg/R/BallBearing.R |only sglg-0.2.3/sglg/R/aux_fs.R | 8 - sglg-0.2.3/sglg/R/claims.R |only sglg-0.2.3/sglg/R/deviance_residuals.R | 2 sglg-0.2.3/sglg/R/dk_order_glg.R |only sglg-0.2.3/sglg/R/glg.R | 234 ++++++++++-------------------- sglg-0.2.3/sglg/R/influence.sglg.R | 63 +------- sglg-0.2.3/sglg/R/moors_lss.R |only sglg-0.2.3/sglg/R/mrl_gg.R |only sglg-0.2.3/sglg/R/order_glg.R | 1 sglg-0.2.3/sglg/R/pk_order_glg.R |only sglg-0.2.3/sglg/R/quantile_residuals.R | 10 - sglg-0.2.3/sglg/R/response_scheme.R |only sglg-0.2.3/sglg/R/rglg.R | 10 - sglg-0.2.3/sglg/R/sglg.R | 4 sglg-0.2.3/sglg/R/shape.R | 6 sglg-0.2.3/sglg/R/slicing_exercises.R |only sglg-0.2.3/sglg/R/summary.sglg.R | 38 ++-- sglg-0.2.3/sglg/R/survglg.R | 18 +- sglg-0.2.3/sglg/R/survival_glg.R | 2 sglg-0.2.3/sglg/data |only sglg-0.2.3/sglg/man/ballbearing.Rd |only sglg-0.2.3/sglg/man/claims.Rd |only sglg-0.2.3/sglg/man/cweight_scheme.Rd |only sglg-0.2.3/sglg/man/deviance_residuals.Rd | 76 ++++----- sglg-0.2.3/sglg/man/dk_order_glg.Rd |only sglg-0.2.3/sglg/man/glg.Rd | 10 - sglg-0.2.3/sglg/man/moors_lss.Rd |only sglg-0.2.3/sglg/man/mrl_gg.Rd |only sglg-0.2.3/sglg/man/order_glg.Rd | 1 sglg-0.2.3/sglg/man/pk_order_glg.Rd |only sglg-0.2.3/sglg/man/quantile_sglg.Rd |only sglg-0.2.3/sglg/man/response_scheme.Rd |only sglg-0.2.3/sglg/man/rglg.Rd | 3 sglg-0.2.3/sglg/man/sglg.Rd | 2 sglg-0.2.3/sglg/man/shape.Rd | 4 sglg-0.2.3/sglg/man/survglg.Rd | 14 + sglg-0.2.3/sglg/man/survival_gg.Rd | 2 sglg-0.2.3/sglg/man/t_lambda.Rd |only sglg-0.2.3/sglg/tests/testthat/test_glg.R | 2 45 files changed, 260 insertions(+), 348 deletions(-)
Title: Convert Files to Parquet Format
Description: Collection of functions to get files in parquet format.
Parquet is a columnar storage file format <https://parquet.apache.org/>.
The files to convert can be of several formats
("csv", "RData", "rds", "RSQLite",
"json", "ndjson", "SAS", "SPSS"...).
Author: Damien Dotta [aut, cre],
Nicolas Chuche [aut]
Maintainer: Damien Dotta <damien.dotta@live.fr>
This is a re-admission after prior archival of version 0.5.7 dated 2024-03-04
Diff between parquetize versions 0.5.7 dated 2024-03-04 and 0.5.8 dated 2025-11-27
parquetize-0.5.7/parquetize/tests/testthat/_snaps |only parquetize-0.5.8/parquetize/DESCRIPTION | 11 + parquetize-0.5.8/parquetize/MD5 | 56 +++++----- parquetize-0.5.8/parquetize/NAMESPACE | 2 parquetize-0.5.8/parquetize/NEWS.md | 6 + parquetize-0.5.8/parquetize/R/csv_to_parquet.R | 2 parquetize-0.5.8/parquetize/R/get_parquet_info.R |only parquetize-0.5.8/parquetize/R/package-parquetize.R | 1 parquetize-0.5.8/parquetize/README.md | 3 parquetize-0.5.8/parquetize/build/vignette.rds |binary parquetize-0.5.8/parquetize/inst/doc/aa-conversions.R | 46 ++++---- parquetize-0.5.8/parquetize/inst/doc/aa-conversions.Rmd | 5 parquetize-0.5.8/parquetize/inst/doc/aa-conversions.html | 33 +---- parquetize-0.5.8/parquetize/man/check_parquet.Rd | 24 ++-- parquetize-0.5.8/parquetize/man/csv_to_parquet.Rd | 14 +- parquetize-0.5.8/parquetize/man/dbi_to_parquet.Rd | 8 - parquetize-0.5.8/parquetize/man/download_extract.Rd | 8 - parquetize-0.5.8/parquetize/man/fst_to_parquet.Rd | 8 - parquetize-0.5.8/parquetize/man/get_parquet_info.Rd |only parquetize-0.5.8/parquetize/man/get_partitions.Rd | 4 parquetize-0.5.8/parquetize/man/json_to_parquet.Rd | 8 - parquetize-0.5.8/parquetize/man/parquetize_example.Rd | 4 parquetize-0.5.8/parquetize/man/rbind_parquet.Rd | 6 - parquetize-0.5.8/parquetize/man/rds_to_parquet.Rd | 8 - parquetize-0.5.8/parquetize/man/sqlite_to_parquet.Rd | 8 - parquetize-0.5.8/parquetize/man/table_to_parquet.Rd | 18 +-- parquetize-0.5.8/parquetize/man/write_parquet_at_once.Rd | 2 parquetize-0.5.8/parquetize/man/write_parquet_by_chunk.Rd | 14 +- parquetize-0.5.8/parquetize/tests/testthat/test-get_parquet_info.R |only parquetize-0.5.8/parquetize/tests/testthat/test-testthat-helpers.R | 2 parquetize-0.5.8/parquetize/vignettes/aa-conversions.Rmd | 5 31 files changed, 160 insertions(+), 146 deletions(-)
Title: Analysing and Plotting Genotype-Phenotype Maps
Description: Tools for studying genotype-phenotype maps for bi-allelic loci underlying quantitative phenotypes. The 0.1 version is released in connection with the publication of Gjuvsland et al (2013) and implements basic line plots and the monotonicity measures for GP maps presented in the paper. Reference: Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Frontier in Genetics 4:216 <doi:10.3389/fgene.2013.00216>.
Author: Arne B. Gjuvsland [aut, cre],
Yunpeng Wang [aut]
Maintainer: Arne B. Gjuvsland <arne.gjuvsland@nmbu.no>
Diff between gpmap versions 0.1.2 dated 2021-02-15 and 0.1.3 dated 2025-11-27
DESCRIPTION | 18 ++++++++----- MD5 | 21 ++++++++------- R/gpmaps.R | 56 +++++++++++++++++++++--------------------- build |only man/GPmaps.Rd | 4 +-- man/decompose_monotone.Rd | 2 - man/degree_of_monotonicity.Rd | 2 - man/enumerate_genotypes.Rd | 2 - man/generate_gpmap.Rd | 2 - man/gpmap-package.Rd | 8 +++--- man/monotone_regression.Rd | 2 - man/partial_genotype_order.Rd | 2 - 12 files changed, 62 insertions(+), 57 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-24 0.1.2
2023-04-24 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-10 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-29 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-05 0.5.0
2020-11-09 0.3.2
2020-11-04 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-04 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-11 1.0.0
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.1 dated 2025-11-11 and 1.1.2 dated 2025-11-27
DESCRIPTION | 11 LICENSE | 4 MD5 | 101 NAMESPACE | 48 NEWS.md | 4 R/global-variables.R | 24 R/ids_bulk.R | 580 +- R/ids_bulk_files.R | 80 R/ids_bulk_series.R | 84 R/ids_get.R | 1082 ++-- R/ids_get_ed.R |only R/ids_list_counterparts.R | 58 R/ids_list_entities.R | 130 R/ids_list_series.R | 56 R/ids_list_series_topics.R | 48 R/perform_request.R | 208 R/read_bulk_info.R | 42 R/sysdata.R | 54 R/wbids-package.R | 27 README.md | 336 - build/vignette.rds |binary inst/doc/data-model.R | 94 inst/doc/data-model.html | 6150 ++++++++++++++------------- inst/doc/data-model.qmd | 250 - man/counterparts.Rd | 32 man/entities.Rd | 32 man/ids_bulk.Rd | 116 man/ids_bulk_files.Rd | 58 man/ids_bulk_series.Rd | 68 man/ids_get.Rd | 288 - man/ids_get_ed.Rd |only man/ids_list_counterparts.Rd | 66 man/ids_list_entities.Rd | 88 man/ids_list_geographies.Rd | 90 man/ids_list_series.Rd | 64 man/ids_list_series_topics.Rd | 56 man/read_bulk_info.Rd | 32 man/series.Rd | 32 man/series_topics.Rd | 32 man/wbids-package.Rd | 70 tests/testthat.R | 24 tests/testthat/test-ids_bulk.R | 808 +-- tests/testthat/test-ids_bulk_files.R | 30 tests/testthat/test-ids_bulk_series.R | 36 tests/testthat/test-ids_get.R | 1292 ++--- tests/testthat/test-ids_get_ed.R |only tests/testthat/test-ids_list_counterparts.R | 20 tests/testthat/test-ids_list_entities.R | 48 tests/testthat/test-ids_list_series.R | 18 tests/testthat/test-ids_list_series_topics.R | 16 tests/testthat/test-perform_request.R | 230 - tests/testthat/test-read_bulk_info.R | 28 vignettes/data-model.qmd | 250 - 53 files changed, 6866 insertions(+), 6529 deletions(-)
Title: Green Index Quantification, Analysis and Visualization
Description: Quantification, analysis, and visualization of urban greenness within city networks using data from 'OpenStreetMap' <https://www.openstreetmap.org>.
Author: Sachit Mahajan [aut, cre]
Maintainer: Sachit Mahajan <sachitmahajan90@gmail.com>
Diff between greenR versions 0.0.1.4 dated 2025-09-08 and 0.0.1.5 dated 2025-11-27
DESCRIPTION | 12 +-- MD5 | 16 ++-- NAMESPACE | 70 ++++++++++++++++++++ R/analyze_and_visualize_uhi.R |only build/vignette.rds |binary inst/doc/introduction.R | 44 +++++++++++++ inst/doc/introduction.Rmd | 76 +++++++++++++++++++++- inst/doc/introduction.html | 131 +++++++++++++++++++++++++++++++-------- man/analyze_and_visualize_uhi.Rd |only vignettes/introduction.Rmd | 76 +++++++++++++++++++++- 10 files changed, 380 insertions(+), 45 deletions(-)
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves, epigantt charts, and diverging bar charts
using 'ggplot2'. Prepare data for visualisation or other reporting for
infectious disease surveillance and outbreak investigation (time
series data). Includes tidy functions to solve date based
transformations for common reporting tasks, like (A) seasonal date
alignment for respiratory disease surveillance, (B) date-based case
binning based on specified time intervals like isoweek, epiweek, month
and more, (C) automated detection and marking of the new year based on
the date/datetime axis of the 'ggplot2', (D) labelling of the last
value of a time-series. An introduction on how to use epicurves can
be found on the US CDC website (2012,
<https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.5.1 dated 2025-07-02 and 0.5.2 dated 2025-11-27
DESCRIPTION | 8 MD5 | 115 ++++----- NEWS.md | 14 - R/align_dates_seasonal.R | 12 R/bin_by_date.R | 5 R/create_agegroups.R | 52 ++-- R/geom_bar_range.R | 7 R/geom_epicurve.R | 5 R/ggplot_theme_helpers.R | 3 R/guide_axis_nested_date.R | 15 - R/label.R | 41 ++- R/scale_cases_5er.R | 30 +- R/stat_last_value.R | 30 +- R/themes.R | 31 -- README.md | 6 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/Epicurves_with_ggsurveillance.html | 7 inst/doc/Epigantt_with_ggsurveillance.html | 9 inst/doc/align_dates_seasonal.html | 5 man/align_dates_seasonal.Rd | 4 man/create_agegroups.Rd | 14 - man/geom_bar_diverging.Rd | 6 man/geom_col_range.Rd | 6 man/geom_epicurve.Rd | 13 - man/geom_epigantt.Rd | 6 man/label_power10.Rd | 6 man/scale_y_cases_5er.Rd | 4 man/stat_last_value.Rd | 6 tests/testthat/_snaps/geom_bar_diverging/1-geom-bar-diverging-basic-horizontal.svg | 24 - tests/testthat/_snaps/geom_bar_diverging/1-geom-bar-diverging-basic-vertical.svg | 24 - tests/testthat/_snaps/geom_bar_diverging/1-geom-bar-diverging-proportion.svg | 24 - tests/testthat/_snaps/geom_bar_diverging/4-complex-diverging-plot.svg | 80 +++--- tests/testthat/_snaps/geom_epicurve/1-geom-epicurve-basic-date.svg | 44 +-- tests/testthat/_snaps/geom_epicurve/1-geom-epicurve-basic-week.svg |only tests/testthat/_snaps/geom_epicurve/2-geom-epicurve-date-resolutionna.svg | 4 tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-epiyear.svg | 4 tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-isoyear.svg | 4 tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-year.svg | 4 tests/testthat/_snaps/geom_epigantt/3-geom-epigantt-full-flip-aes.svg | 2 tests/testthat/_snaps/geom_epigantt/3-geom-epigantt-full.svg | 2 tests/testthat/_snaps/label_power10 |only tests/testthat/_snaps/stat_last_value/2-geom-text-last-value-basic.svg | 2 tests/testthat/_snaps/stat_last_value/2-geom-text-last-value-label.svg |only tests/testthat/_snaps/stat_last_value/2-geom-text-last-value-labeller.svg | 2 tests/testthat/_snaps/stat_last_value/2-geom-text-last-value-percent.svg | 2 tests/testthat/_snaps/stat_last_value/3-geom-label-last-value-basic.svg | 4 tests/testthat/_snaps/stat_last_value/3-geom-label-last-value-nudge.svg | 4 tests/testthat/_snaps/stat_last_value/4-geom-text-last-value-repel-labeller.svg |only tests/testthat/_snaps/stat_last_value/4-geom-text-last-value-repel-min-segment.svg | 6 tests/testthat/_snaps/stat_last_value/5-geom-label-last-value-repel-basic.svg | 4 tests/testthat/_snaps/stat_last_value/5-geom-label-last-value-repel-custom.svg | 4 tests/testthat/_snaps/stat_last_value/6-stat-last-value-abs-nudge-date.svg | 2 tests/testthat/_snaps/stat_last_value/6-stat-last-value-abs-nudge-datetime.svg | 4 tests/testthat/_snaps/stat_last_value/7-stat-last-value-na-at-end.svg | 4 tests/testthat/test-create_agegroups.R | 16 + tests/testthat/test-geom_epicurve.R | 27 +- tests/testthat/test-label_power10.R | 126 ++++++++++ tests/testthat/test-stat_last_value.R | 28 ++ 59 files changed, 599 insertions(+), 313 deletions(-)
More information about ggsurveillance at CRAN
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Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models.
References, <https://journal.r-project.org/articles/RJ-2025-018/>.
Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>.
Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>.
Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>.
Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>.
Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>.
Santolino, M. (2023) <d [...truncated...]
Author: David Atance [aut, cre] ,
Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>
Diff between CvmortalityMult versions 1.1.0 dated 2025-05-09 and 1.1.1 dated 2025-11-27
DESCRIPTION | 10 MD5 | 12 R/fitLCmulti.R | 2 R/multipopulation_cv.R | 11 README.md | 2 man/fitLCmulti.Rd | 2 man/multipopulation_cv.Rd | 687 +++++++++++++++++++++++----------------------- 7 files changed, 367 insertions(+), 359 deletions(-)
More information about CvmortalityMult at CRAN
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Title: Generalized Kumaraswamy Regression Models for Bounded Data
Description: Implements regression models for bounded continuous data in the open interval (0,1) using the five-parameter Generalized Kumaraswamy distribution. Supports modeling all distribution parameters (alpha, beta, gamma, delta, lambda) as functions of predictors through various link functions. Provides efficient maximum likelihood estimation via Template Model Builder ('TMB'), offering comprehensive diagnostics, model comparison tools, and simulation methods. Particularly useful for analyzing proportions, rates, indices, and other bounded response data with complex distributional features not adequately captured by simpler models.
Author: Jose Evandeilton Lopes [aut, cre]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between gkwreg versions 2.1.1 dated 2025-11-15 and 2.1.6 dated 2025-11-27
gkwreg-2.1.1/gkwreg/src/gkwreg-predict-resid.cpp |only gkwreg-2.1.6/gkwreg/DESCRIPTION | 6 gkwreg-2.1.6/gkwreg/MD5 | 58 gkwreg-2.1.6/gkwreg/NAMESPACE | 4 gkwreg-2.1.6/gkwreg/NEWS.md | 13 gkwreg-2.1.6/gkwreg/R/RcppExports.R | 2 gkwreg-2.1.6/gkwreg/R/gkwreg-compile-tmb.R |only gkwreg-2.1.6/gkwreg/R/gkwreg-plot.R | 19 gkwreg-2.1.6/gkwreg/R/zzz.R | 467 ---- gkwreg-2.1.6/gkwreg/README.md | 294 +- gkwreg-2.1.6/gkwreg/inst/doc/gkwreg-vs-betareg.html | 50 gkwreg-2.1.6/gkwreg/inst/paper/paper.log | 48 gkwreg-2.1.6/gkwreg/inst/paper/paper.md | 60 gkwreg-2.1.6/gkwreg/inst/paper/paper.pdf |binary gkwreg-2.1.6/gkwreg/inst/tmb/bkwreg.cpp | 572 ----- gkwreg-2.1.6/gkwreg/inst/tmb/ekwreg.cpp | 566 ----- gkwreg-2.1.6/gkwreg/inst/tmb/gkwbetareg.cpp | 478 ---- gkwreg-2.1.6/gkwreg/inst/tmb/gkwreg.cpp | 1095 ----------- gkwreg-2.1.6/gkwreg/inst/tmb/kkwreg.cpp | 603 ------ gkwreg-2.1.6/gkwreg/inst/tmb/kwreg.cpp | 2 gkwreg-2.1.6/gkwreg/inst/tmb/mcreg.cpp | 549 ----- gkwreg-2.1.6/gkwreg/man/clean_tmb_cache.Rd |only gkwreg-2.1.6/gkwreg/man/dot-check_and_compile_TMB_code.Rd | 37 gkwreg-2.1.6/gkwreg/man/dot-compile_model.Rd |only gkwreg-2.1.6/gkwreg/man/dot-get_cache_dir.Rd |only gkwreg-2.1.6/gkwreg/man/dot-is_dll_functional.Rd |only gkwreg-2.1.6/gkwreg/man/dot-load_dll.Rd |only gkwreg-2.1.6/gkwreg/man/list_tmb_models.Rd |only gkwreg-2.1.6/gkwreg/man/precompile_tmb_models.Rd |only gkwreg-2.1.6/gkwreg/src/Makevars | 6 gkwreg-2.1.6/gkwreg/src/Makevars.win | 12 gkwreg-2.1.6/gkwreg/src/RcppExports.cpp | 8 gkwreg-2.1.6/gkwreg/src/gkwregPredictResid.cpp |only gkwreg-2.1.6/gkwreg/tests/testthat/test-gkwreg-anova-tests.R | 80 gkwreg-2.1.6/gkwreg/tests/testthat/test-gkwreg-plot-tests.R | 36 35 files changed, 451 insertions(+), 4614 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: Wu LI [aut, cre]
Maintainer: Wu LI <liwu.shu@qq.com>
Diff between GE versions 0.5.0 dated 2025-06-19 and 0.5.3 dated 2025-11-27
GE-0.5.0/GE/R/gemIntertemporal_EndogenousEquilibriumInterestRate_MoneyVelocity.R |only GE-0.5.0/GE/R/gemOLG_Land_4_3.R |only GE-0.5.0/GE/man/gemIntertemporal_EndogenousEquilibriumInterestRate_MoneyVelocity.Rd |only GE-0.5.0/GE/man/gemOLG_Land_4_3.Rd |only GE-0.5.3/GE/DESCRIPTION | 10 GE-0.5.3/GE/MD5 | 20 GE-0.5.3/GE/NAMESPACE | 2 GE-0.5.3/GE/R/ge_tidy.R | 11 GE-0.5.3/GE/R/gemIntertemporal_EndogenousEquilibriumInterestRate.R | 232 +++--- GE-0.5.3/GE/R/gemIntertemporal_EndogenousEquilibriumInterestRate__ForeignExchangeRate.R | 360 ++-------- GE-0.5.3/GE/R/sdm2.R | 14 GE-0.5.3/GE/man/gemIntertemporal_EndogenousEquilibriumInterestRate.Rd | 233 +++--- GE-0.5.3/GE/man/gemIntertemporal_EndogenousEquilibriumInterestRate_ForeignExchangeRate.Rd | 356 ++------- 13 files changed, 470 insertions(+), 768 deletions(-)
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 2.1.1 dated 2025-02-19 and 2.1.2 dated 2025-11-27
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/walkthrough.pdf |binary src/ensemble.h | 2 +- src/interface.h | 2 +- src/vistla.c | 6 ++++++ 8 files changed, 24 insertions(+), 13 deletions(-)
Title: Topic Modelling in Embedding Spaces
Description: Find topics in texts which are semantically embedded using techniques like word2vec or Glove.
This topic modelling technique models each word with a categorical distribution whose natural parameter is the inner product between a word embedding and an embedding of its assigned topic.
The techniques are explained in detail in the paper 'Topic Modeling in Embedding Spaces' by Adji B. Dieng, Francisco J. R. Ruiz, David M. Blei (2019), available at <doi:10.48550/arXiv.1907.04907>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Adji B. Dieng [ctb, cph] ,
Francisco J. R. Ruiz [ctb, cph] ,
David M. Blei [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between topicmodels.etm versions 0.1.0 dated 2021-11-08 and 0.1.1 dated 2025-11-27
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/ETM.R | 43 +++++++++++++++++++++++++++++++------------ man/ETM.Rd | 28 ++++++++++++++++++---------- man/plot.ETM.Rd | 9 ++++++--- man/summary.ETM.Rd | 6 +++++- 7 files changed, 81 insertions(+), 38 deletions(-)
More information about topicmodels.etm at CRAN
Permanent link
Title: Command Line Interface Plotting
Description: The 'plotcli' package provides terminal-based plotting in R.
It supports colored scatter plots, line plots, bar plots, boxplots,
histograms, density plots, and more. The 'ggplotcli()' function is a
universal converter that renders any 'ggplot2' plot in the terminal
using Unicode Braille characters or ASCII. Features include support for
15+ geom types, faceting (facet_wrap/facet_grid), automatic theme
detection, legends, optimized color mapping, and multiple canvas types.
Author: Claas Heuer [aut, cre]
Maintainer: Claas Heuer <claasheuer@gmail.com>
Diff between plotcli versions 0.1.0 dated 2024-04-24 and 0.2.0 dated 2025-11-27
DESCRIPTION | 22 +- MD5 | 90 +++++++-- NAMESPACE | 33 ++- NEWS.md |only R/canvas.r |only R/geom_registry.r |only R/ggplotcli.r | 241 +++++++++++++++----------- R/ggplotcli_helpers.r |only R/helper_functions.r | 103 +++++++++++ R/plotcli.r | 232 ++++++++++--------------- README.md | 167 ++++++++++++------ build/vignette.rds |binary inst/doc/ggplotcli.R |only inst/doc/ggplotcli.Rmd |only inst/doc/ggplotcli.html |only inst/doc/ggplotli.R | 97 +++++++++- inst/doc/ggplotli.Rmd | 148 +++++++++++++++- inst/doc/ggplotli.html | 376 ++++++++++++++++++++++++++++++++--------- inst/doc/plotcli_class.Rmd | 4 inst/doc/plotcli_class.html | 77 ++++---- inst/doc/plotcli_wrappers.Rmd | 4 inst/doc/plotcli_wrappers.html | 95 +++++----- man/AsciiCanvas.Rd |only man/BlockCanvas.Rd |only man/BrailleCanvas.Rd |only man/Canvas.Rd |only man/GeomRegistry.Rd |only man/add_legend_to_output.Rd |only man/braille_dot_bit.Rd |only man/braille_set_dot.Rd |only man/build_plot_output.Rd |only man/build_plot_output_v2.Rd |only man/color_to_term.Rd |only man/create_canvas.Rd |only man/create_panel_scales.Rd |only man/create_scales.Rd |only man/dot-geom_registry.Rd |only man/draw_border.Rd |only man/draw_grid.Rd |only man/extract_legend_info.Rd |only man/extract_plot_labels.Rd |only man/extract_plot_style.Rd |only man/format_axis_label.Rd |only man/geom_area_handler.Rd |only man/geom_bar_handler.Rd |only man/geom_boxplot_handler.Rd |only man/geom_density_handler.Rd |only man/geom_histogram_handler.Rd |only man/geom_hline_handler.Rd |only man/geom_line_handler.Rd |only man/geom_path_handler.Rd |only man/geom_point_handler.Rd |only man/geom_rect_handler.Rd |only man/geom_segment_handler.Rd |only man/geom_smooth_handler.Rd |only man/geom_text_handler.Rd |only man/geom_vline_handler.Rd |only man/get_color_hue.Rd |only man/get_facet_info.Rd |only man/get_geom_handler.Rd |only man/ggplotcli.Rd | 76 +++++++- man/init_color_mapping.Rd |only man/is_geom_registered.Rd |only man/list_registered_geoms.Rd |only man/pixel_to_braille.Rd |only man/register_geom.Rd |only man/render_faceted_plot.Rd |only man/render_single_panel.Rd |only man/safe_aes_name.Rd |only vignettes/ggplotcli.Rmd |only vignettes/ggplotli.Rmd | 148 +++++++++++++++- vignettes/plotcli_class.Rmd | 4 vignettes/plotcli_wrappers.Rmd | 4 73 files changed, 1401 insertions(+), 520 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Feature selection package of the 'mlr3' ecosystem. It selects
the optimal feature set for any 'mlr3' learner. The package works with
several optimization algorithms e.g. Random Search, Recursive Feature
Elimination, and Genetic Search. Moreover, it can automatically
optimize learners and estimate the performance of optimized feature
sets with nested resampling.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 1.4.0 dated 2025-07-31 and 1.5.0 dated 2025-11-27
DESCRIPTION | 12 +- MD5 | 44 ++++---- NAMESPACE | 1 NEWS.md | 5 R/EnsembleFSResult.R | 1 R/ObjectiveFSelectAsync.R | 10 + R/ObjectiveFSelectBatch.R | 10 + R/faggregate.R |only R/zzz.R | 8 - README.md | 21 +++- inst/testthat/helper_misc.R | 12 +- man/ensemble_fs_result.Rd | 2 man/faggregate.Rd |only man/mlr_fselectors_genetic_search.Rd | 2 tests/testthat/test_ArchiveAsyncFSelect.R | 50 +-------- tests/testthat/test_ArchiveAsyncFSelectFrozen.R | 4 tests/testthat/test_AutoFSelector.R | 2 tests/testthat/test_CallbackAsyncFSelect.R | 85 +++------------- tests/testthat/test_FSelectInstanceAsyncMultiCrit.R | 25 ---- tests/testthat/test_FSelectInstanceAsyncSingleCrit.R | 21 ---- tests/testthat/test_ObjectiveFSelect.R | 82 +++++++++++++++- tests/testthat/test_ObjectiveFSelectAsync.R | 97 +++++++++++++++++++ tests/testthat/test_auto_fselector.R | 1 tests/testthat/test_mlr_callbacks.R | 5 24 files changed, 299 insertions(+), 201 deletions(-)
Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized
large-N trials with the 'tricot' approach <https://climmob.net/>.
Developed by van Etten et al. (2019) <doi:10.1017/S0014479716000739>, it turns the
research paradigm on its head; instead of a few researchers designing complicated
trials to compare several technologies in search of the best solutions for the
target environment, it enables many participants to carry out reasonably simple
experiments that taken together can offer even more information. 'ClimMobTools'
enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between ClimMobTools versions 1.8 dated 2025-11-15 and 1.8.2 dated 2025-11-27
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 28 +++++++++++++- R/exportMeasuredTraits.R | 69 ++++++++++++++++++++++++----------- R/getProjectsCM.R | 86 ++++++++++++++++++++++++++------------------ man/exportMeasuredTraits.Rd | 9 +++- 6 files changed, 142 insertions(+), 66 deletions(-)
Title: Create Non-Confidential Multi-Resolution Grids
Description: The need for anonymization of individual survey responses often leads to many suppressed grid cells in a regular grid. Here we provide functionality for creating multi-resolution gridded data, respecting the confidentiality rules, such as a minimum number of units and dominance by one or more units for each grid cell. The functions also include the possibility for contextual suppression of data. For more details see Skoien et al. (2025) <doi:10.48550/arXiv.2410.17601>.
Author: Jon Olav Skoien [aut, cre],
Nicolas Lampach [aut]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between MRG versions 0.3.10 dated 2025-07-11 and 0.3.21 dated 2025-11-27
DESCRIPTION | 18 +-- MD5 | 58 ++++++------ NAMESPACE | 9 + R/MRGmerge.R | 148 ++++++++++++++++++++++++-------- R/MRGoverlap.R | 30 ++---- R/MRGplot.R | 12 +- R/MRGpostProcess.R | 2 R/confid.R | 2 R/createMRGobject.R | 42 +++++++-- R/fssgeo.R | 21 +++- R/gridData.R | 44 +++++---- R/inspireID.R |only R/multiResGrid.R | 38 +++----- R/remSmall.R | 195 +++++++++++++++++++++---------------------- R/roxygen_eval.R | 37 ++++++-- R/zzz.R |only build/vignette.rds |binary data/ifs_dk.rda |binary inst/doc/MRG.html | 18 +-- inst/ex/dkb.rda |only man/MRGmerge.Rd | 58 ++++++++++++ man/MRGoverlap.Rd | 33 +++---- man/MRGplot.Rd | 12 +- man/MRGpostProcess.Rd | 2 man/createMRGobject.Rd | 30 +++++- man/fssgeo.Rd | 4 man/gridData.Rd | 21 ++-- man/inspireID.Rd |only man/multiResGrid.Rd | 29 +++--- man/remSmall.Rd | 177 +++++++++++++++++++-------------------- tests/multiResGrid.R | 14 ++- tests/multiResGrid.Rout.save | 25 ++++- 32 files changed, 663 insertions(+), 416 deletions(-)
Title: Distributed Representations of Sentences, Documents and Topics
Description: Learn vector representations of sentences, paragraphs or documents by using the 'Paragraph Vector' algorithms,
namely the distributed bag of words ('PV-DBOW') and the distributed memory ('PV-DM') model.
The techniques in the package are detailed in the paper "Distributed Representations of Sentences and Documents" by Mikolov et al. (2014), available at <doi:10.48550/arXiv.1405.4053>.
The package also provides an implementation to cluster documents based on these embedding using a technique called top2vec.
Top2vec finds clusters in text documents by combining techniques to embed documents and words and density-based clustering.
It does this by embedding documents in the semantic space as defined by the 'doc2vec' algorithm. Next it maps
these document embeddings to a lower-dimensional space using the 'Uniform Manifold Approximation and Projection' (UMAP) clustering algorithm
and finds dense areas in that space using a 'Hierarchical Density-Based Clustering' technique (HDBSCAN). The [...truncated...]
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
hiyijian [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between doc2vec versions 0.2.0 dated 2021-03-27 and 0.2.2 dated 2025-11-27
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 10 ++++++++++ R/paragraph2vec.R | 16 +++++++++++++++- R/top2vec.R | 2 -- README.md | 10 ++++++++-- man/paragraph2vec.Rd | 3 ++- man/top2vec.Rd | 2 -- src/Makevars | 1 - 9 files changed, 49 insertions(+), 23 deletions(-)
Title: A Toolbox for Clinical Significance Analyses in Intervention
Studies
Description: A clinical significance analysis can be used to determine if an
intervention has a meaningful or practical effect for patients. You provide
a tidy data set plus a few more metrics and this package will take care of
it to make your results publication ready. Accompanying package to
Claus et al. <doi:10.18637/jss.v111.i01>.
Author: Benedikt Claus [aut, cre]
Maintainer: Benedikt Claus <benediktclaus@outlook.com>
Diff between clinicalsignificance versions 2.1.0 dated 2024-12-02 and 3.0.0 dated 2025-11-27
DESCRIPTION | 25 - MD5 | 91 ++-- NEWS.md | 13 R/create_summary_table.R | 216 +++++++---- R/cs_anchor.R | 417 +++++++++++++-------- R/cs_combined.R | 296 +++++++++------ R/cs_distribution.R | 185 +++++---- R/cs_get_summary.R | 20 - R/cs_percentage.R | 184 +++++---- R/cs_statistical.R | 188 ++++++--- R/datasets.R | 112 +++++ R/globals.R | 103 ++++- R/package-utils.R | 93 ++++ README.md | 304 +++++++-------- build/vignette.rds |binary data/columbo.rda |only data/garden_club.rda |only data/garden_club_sensitive.rda |only data/trackmania.rda |only inst/doc/anchor-based-approach.R | 104 +---- inst/doc/anchor-based-approach.Rmd | 198 ++++------ inst/doc/anchor-based-approach.html | 586 ++++++++++++------------------ inst/doc/combined-approach.R | 128 +----- inst/doc/combined-approach.Rmd | 218 +++-------- inst/doc/combined-approach.html | 582 ++++++++++------------------- inst/doc/distribution-based-approach.R | 118 +----- inst/doc/distribution-based-approach.Rmd | 189 +++------ inst/doc/distribution-based-approach.html | 520 +++++++++----------------- inst/doc/percentage-change-approach.R | 111 +---- inst/doc/percentage-change-approach.Rmd | 179 ++------- inst/doc/percentage-change-approach.html | 458 +++++++---------------- inst/doc/statistical-approach.R | 98 +---- inst/doc/statistical-approach.Rmd | 179 +++------ inst/doc/statistical-approach.html | 492 +++++++++---------------- man/columbo.Rd |only man/figures/README-example-1.png |only man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/figures/logo.png |binary man/garden_club.Rd |only man/garden_club_sensitive.Rd |only man/trackmania.Rd |only tests/testthat/_snaps/cs_combined.md | 368 +++++++++--------- tests/testthat/_snaps/cs_distribution.md | 314 ++++++++-------- tests/testthat/_snaps/cs_percentage.md | 81 ++-- vignettes/anchor-based-approach.Rmd | 198 ++++------ vignettes/combined-approach.Rmd | 218 +++-------- vignettes/distribution-based-approach.Rmd | 189 +++------ vignettes/percentage-change-approach.Rmd | 179 ++------- vignettes/statistical-approach.Rmd | 179 +++------ 51 files changed, 3604 insertions(+), 4529 deletions(-)
More information about clinicalsignificance at CRAN
Permanent link
Title: Bayesian Regression for Dynamic Treatment Regimes
Description: Methods to estimate optimal dynamic treatment regimes using Bayesian
likelihood-based regression approach as described in
Yu, W., & Bondell, H. D. (2023) <doi:10.1093/jrsssb/qkad016>
Uses backward induction and dynamic programming theory for computing
expected values. Offers options for future parallel computing.
Author: Jeremy Lim [aut],
Weichang Yu [aut, cre]
Maintainer: Weichang Yu <weichang.yu@unimelb.edu.au>
Diff between BayesRegDTR versions 1.1.1 dated 2025-10-26 and 1.1.2 dated 2025-11-27
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 14 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-28 1.1.2
2024-06-05 1.1.1
2024-04-25 1.1.0
2023-12-13 1.0.5
2023-11-10 1.0.4
2023-07-20 1.0.3
2023-07-07 1.0.2
2023-06-29 1.0.1
2023-06-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-19 0.2.2
2022-02-28 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-12 1.1
2015-02-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-10 1.1.0
2021-08-17 1.0.0
2015-05-21 0.3-1
2013-06-14 0.2-1
2011-11-02 0.1-7
2011-05-28 0.1-6
2011-03-22 0.1-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-14 1.2.2
2021-03-31 1.2.1
2020-11-19 1.2.0
2020-07-26 1.1.1
2020-05-01 1.1.0
2019-09-27 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-13 1.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-13 1.0.0
2024-09-13 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-03 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-18 1.0.0.10
2022-08-19 1.0.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-16 1.0.1
2022-08-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-25 0.2.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-14 1.16
2024-01-29 1.15
2022-04-22 1.12
2022-01-21 1.11
2022-01-11 1.10
2020-05-22 1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-02 2.1.0
2020-03-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-10 0.1.1
2019-10-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-14 0.94.1
2017-02-03 0.94
2016-11-10 0.92
2016-08-09 0.90
2016-05-26 0.88
2015-02-18 0.86
2013-12-20 0.84.1
2013-10-25 0.84
2012-12-10 0.81
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-27 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-19 0.1
Title: A 'Linter' for R Code
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with
'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual
Studio Code'.
Author: Jim Hester [aut],
Florent Angly [aut] ,
Russ Hyde [aut],
Michael Chirico [aut, cre] ,
Kun Ren [aut],
Alexander Rosenstock [aut] ,
Indrajeet Patil [aut] ,
Hugo Gruson [aut]
Maintainer: Michael Chirico <michaelchirico4@gmail.com>
Diff between lintr versions 3.2.0 dated 2025-02-12 and 3.3.0-1 dated 2025-11-27
lintr-3.2.0/lintr/tests/testthat/test-make_linter_from_regex.R |only lintr-3.2.0/lintr/tests/testthat/test-normalize_exclusions.R |only lintr-3.2.0/lintr/tests/testthat/test-parse_exclusions.R |only lintr-3.3.0-1/lintr/DESCRIPTION | 50 - lintr-3.3.0-1/lintr/MD5 | 497 +++++----- lintr-3.3.0-1/lintr/NAMESPACE | 12 lintr-3.3.0-1/lintr/NEWS.md | 161 ++- lintr-3.3.0-1/lintr/R/T_and_F_symbol_linter.R | 10 lintr-3.3.0-1/lintr/R/absolute_path_linter.R | 2 lintr-3.3.0-1/lintr/R/all_equal_linter.R |only lintr-3.3.0-1/lintr/R/any_duplicated_linter.R | 109 +- lintr-3.3.0-1/lintr/R/any_is_na_linter.R | 2 lintr-3.3.0-1/lintr/R/assignment_linter.R | 83 - lintr-3.3.0-1/lintr/R/backport_linter.R | 34 lintr-3.3.0-1/lintr/R/boolean_arithmetic_linter.R | 18 lintr-3.3.0-1/lintr/R/brace_linter.R | 53 - lintr-3.3.0-1/lintr/R/coalesce_linter.R |only lintr-3.3.0-1/lintr/R/comparison_negation_linter.R | 6 lintr-3.3.0-1/lintr/R/condition_call_linter.R | 16 lintr-3.3.0-1/lintr/R/condition_message_linter.R | 2 lintr-3.3.0-1/lintr/R/conjunct_test_linter.R | 5 lintr-3.3.0-1/lintr/R/consecutive_assertion_linter.R | 2 lintr-3.3.0-1/lintr/R/cyclocomp_linter.R | 23 lintr-3.3.0-1/lintr/R/declared_functions.R | 29 lintr-3.3.0-1/lintr/R/download_file_linter.R |only lintr-3.3.0-1/lintr/R/empty_assignment_linter.R | 2 lintr-3.3.0-1/lintr/R/exclude.R | 33 lintr-3.3.0-1/lintr/R/expect_comparison_linter.R | 2 lintr-3.3.0-1/lintr/R/expect_length_linter.R | 4 lintr-3.3.0-1/lintr/R/expect_lint.R | 174 ++- lintr-3.3.0-1/lintr/R/expect_true_false_linter.R | 10 lintr-3.3.0-1/lintr/R/extract.R | 16 lintr-3.3.0-1/lintr/R/fixed_regex_linter.R | 4 lintr-3.3.0-1/lintr/R/function_left_parentheses_linter.R | 3 lintr-3.3.0-1/lintr/R/get_source_expressions.R | 173 ++- lintr-3.3.0-1/lintr/R/ids_with_token.R | 10 lintr-3.3.0-1/lintr/R/if_switch_linter.R | 18 lintr-3.3.0-1/lintr/R/ifelse_censor_linter.R | 11 lintr-3.3.0-1/lintr/R/implicit_assignment_linter.R | 26 lintr-3.3.0-1/lintr/R/implicit_integer_linter.R | 5 lintr-3.3.0-1/lintr/R/indentation_linter.R | 145 +- lintr-3.3.0-1/lintr/R/is_lint_level.R | 2 lintr-3.3.0-1/lintr/R/length_test_linter.R | 39 lintr-3.3.0-1/lintr/R/lengths_linter.R | 2 lintr-3.3.0-1/lintr/R/library_call_linter.R | 15 lintr-3.3.0-1/lintr/R/line_length_linter.R | 97 + lintr-3.3.0-1/lintr/R/lint.R | 263 +++-- lintr-3.3.0-1/lintr/R/linter_tags.R | 20 lintr-3.3.0-1/lintr/R/lintr-deprecated.R | 142 -- lintr-3.3.0-1/lintr/R/lintr-package.R | 9 lintr-3.3.0-1/lintr/R/list2df_linter.R |only lintr-3.3.0-1/lintr/R/literal_coercion_linter.R | 3 lintr-3.3.0-1/lintr/R/make_linter_from_regex.R | 4 lintr-3.3.0-1/lintr/R/matrix_apply_linter.R | 23 lintr-3.3.0-1/lintr/R/methods.R | 64 - lintr-3.3.0-1/lintr/R/missing_argument_linter.R | 7 lintr-3.3.0-1/lintr/R/nzchar_linter.R | 7 lintr-3.3.0-1/lintr/R/object_usage_linter.R | 140 ++ lintr-3.3.0-1/lintr/R/outer_negation_linter.R | 2 lintr-3.3.0-1/lintr/R/package_hooks_linter.R | 20 lintr-3.3.0-1/lintr/R/paren_body_linter.R | 1 lintr-3.3.0-1/lintr/R/paste_linter.R | 8 lintr-3.3.0-1/lintr/R/path_utils.R | 18 lintr-3.3.0-1/lintr/R/pipe_consistency_linter.R | 29 lintr-3.3.0-1/lintr/R/pipe_return_linter.R | 17 lintr-3.3.0-1/lintr/R/redundant_equals_linter.R | 2 lintr-3.3.0-1/lintr/R/regex_subset_linter.R | 53 - lintr-3.3.0-1/lintr/R/repeat_linter.R | 3 lintr-3.3.0-1/lintr/R/return_linter.R | 4 lintr-3.3.0-1/lintr/R/sample_int_linter.R | 2 lintr-3.3.0-1/lintr/R/scalar_in_linter.R | 12 lintr-3.3.0-1/lintr/R/seq_linter.R | 66 + lintr-3.3.0-1/lintr/R/settings.R | 14 lintr-3.3.0-1/lintr/R/settings_utils.R | 3 lintr-3.3.0-1/lintr/R/shared_constants.R | 58 - lintr-3.3.0-1/lintr/R/sort_linter.R | 37 lintr-3.3.0-1/lintr/R/source_utils.R | 21 lintr-3.3.0-1/lintr/R/sprintf_linter.R | 55 - lintr-3.3.0-1/lintr/R/string_boundary_linter.R | 51 - lintr-3.3.0-1/lintr/R/strings_as_factors_linter.R | 4 lintr-3.3.0-1/lintr/R/terminal_close_linter.R | 2 lintr-3.3.0-1/lintr/R/todo_comment_linter.R | 8 lintr-3.3.0-1/lintr/R/trailing_blank_lines_linter.R | 4 lintr-3.3.0-1/lintr/R/undesirable_function_linter.R | 50 - lintr-3.3.0-1/lintr/R/undesirable_operator_linter.R | 80 + lintr-3.3.0-1/lintr/R/unnecessary_concatenation_linter.R | 2 lintr-3.3.0-1/lintr/R/unnecessary_lambda_linter.R | 17 lintr-3.3.0-1/lintr/R/unnecessary_nesting_linter.R | 31 lintr-3.3.0-1/lintr/R/unnecessary_placeholder_linter.R | 2 lintr-3.3.0-1/lintr/R/unused_import_linter.R | 3 lintr-3.3.0-1/lintr/R/use_lintr.R | 30 lintr-3.3.0-1/lintr/R/utils.R | 83 - lintr-3.3.0-1/lintr/R/vector_logic_linter.R | 4 lintr-3.3.0-1/lintr/R/with.R | 29 lintr-3.3.0-1/lintr/R/with_id.R | 9 lintr-3.3.0-1/lintr/R/xml_utils.R | 22 lintr-3.3.0-1/lintr/R/zzz.R | 27 lintr-3.3.0-1/lintr/README.md | 1 lintr-3.3.0-1/lintr/build/stage23.rdb |binary lintr-3.3.0-1/lintr/build/vignette.rds |binary lintr-3.3.0-1/lintr/inst/CITATION |only lintr-3.3.0-1/lintr/inst/doc/lintr.R | 1 lintr-3.3.0-1/lintr/inst/doc/lintr.Rmd | 9 lintr-3.3.0-1/lintr/inst/doc/lintr.html | 262 ++--- lintr-3.3.0-1/lintr/inst/lintr/linters.csv | 22 lintr-3.3.0-1/lintr/man/absolute_path_linter.Rd | 2 lintr-3.3.0-1/lintr/man/all_equal_linter.Rd |only lintr-3.3.0-1/lintr/man/any_duplicated_linter.Rd | 10 lintr-3.3.0-1/lintr/man/any_is_na_linter.Rd | 2 lintr-3.3.0-1/lintr/man/assignment_linter.Rd | 19 lintr-3.3.0-1/lintr/man/backport_linter.Rd | 16 lintr-3.3.0-1/lintr/man/best_practices_linters.Rd | 2 lintr-3.3.0-1/lintr/man/brace_linter.Rd | 17 lintr-3.3.0-1/lintr/man/coalesce_linter.Rd |only lintr-3.3.0-1/lintr/man/common_mistakes_linters.Rd | 2 lintr-3.3.0-1/lintr/man/condition_message_linter.Rd | 2 lintr-3.3.0-1/lintr/man/conjunct_test_linter.Rd | 2 lintr-3.3.0-1/lintr/man/consecutive_assertion_linter.Rd | 2 lintr-3.3.0-1/lintr/man/consistency_linters.Rd | 1 lintr-3.3.0-1/lintr/man/cyclocomp_linter.Rd | 2 lintr-3.3.0-1/lintr/man/default_linters.Rd | 3 lintr-3.3.0-1/lintr/man/default_settings.Rd | 3 lintr-3.3.0-1/lintr/man/default_undesirable_functions.Rd | 2 lintr-3.3.0-1/lintr/man/deprecated_linters.Rd | 10 lintr-3.3.0-1/lintr/man/download_file_linter.Rd |only lintr-3.3.0-1/lintr/man/efficiency_linters.Rd | 1 lintr-3.3.0-1/lintr/man/exclude.Rd | 7 lintr-3.3.0-1/lintr/man/expect_lint.Rd | 23 lintr-3.3.0-1/lintr/man/get_source_expressions.Rd | 1 lintr-3.3.0-1/lintr/man/gitlab_output.Rd |only lintr-3.3.0-1/lintr/man/ids_with_token.Rd | 6 lintr-3.3.0-1/lintr/man/implicit_assignment_linter.Rd | 19 lintr-3.3.0-1/lintr/man/length_test_linter.Rd | 26 lintr-3.3.0-1/lintr/man/lengths_linter.Rd | 2 lintr-3.3.0-1/lintr/man/library_call_linter.Rd | 2 lintr-3.3.0-1/lintr/man/line_length_linter.Rd | 56 + lintr-3.3.0-1/lintr/man/lint-s3.Rd | 5 lintr-3.3.0-1/lintr/man/lint.Rd | 12 lintr-3.3.0-1/lintr/man/linters.Rd | 21 lintr-3.3.0-1/lintr/man/lintr-deprecated.Rd | 48 lintr-3.3.0-1/lintr/man/lintr-package.Rd | 5 lintr-3.3.0-1/lintr/man/list2df_linter.Rd |only lintr-3.3.0-1/lintr/man/matrix_apply_linter.Rd | 22 lintr-3.3.0-1/lintr/man/normalize_exclusions.Rd | 13 lintr-3.3.0-1/lintr/man/object_usage_linter.Rd | 19 lintr-3.3.0-1/lintr/man/package_hooks_linter.Rd | 14 lintr-3.3.0-1/lintr/man/paste_linter.Rd | 8 lintr-3.3.0-1/lintr/man/pipe_consistency_linter.Rd | 25 lintr-3.3.0-1/lintr/man/pipe_return_linter.Rd | 17 lintr-3.3.0-1/lintr/man/readability_linters.Rd | 2 lintr-3.3.0-1/lintr/man/regex_subset_linter.Rd | 19 lintr-3.3.0-1/lintr/man/repeat_linter.Rd | 3 lintr-3.3.0-1/lintr/man/robustness_linters.Rd | 2 lintr-3.3.0-1/lintr/man/scalar_in_linter.Rd | 5 lintr-3.3.0-1/lintr/man/seq_linter.Rd | 20 lintr-3.3.0-1/lintr/man/sprintf_linter.Rd | 5 lintr-3.3.0-1/lintr/man/string_boundary_linter.Rd | 4 lintr-3.3.0-1/lintr/man/undesirable_function_linter.Rd | 30 lintr-3.3.0-1/lintr/man/undesirable_operator_linter.Rd | 47 lintr-3.3.0-1/lintr/tests/testthat/default_linter_testcode.R | 1 lintr-3.3.0-1/lintr/tests/testthat/dummy_projects/project/mismatched_starts_ends.R | 10 lintr-3.3.0-1/lintr/tests/testthat/dummy_projects/project/one_start_no_end.R | 2 lintr-3.3.0-1/lintr/tests/testthat/helper.R | 7 lintr-3.3.0-1/lintr/tests/testthat/test-Lint-builder.R | 20 lintr-3.3.0-1/lintr/tests/testthat/test-T_and_F_symbol_linter.R | 32 lintr-3.3.0-1/lintr/tests/testthat/test-absolute_path_linter.R | 144 -- lintr-3.3.0-1/lintr/tests/testthat/test-all_equal_linter.R |only lintr-3.3.0-1/lintr/tests/testthat/test-any_duplicated_linter.R | 37 lintr-3.3.0-1/lintr/tests/testthat/test-assignment_linter.R | 159 +-- lintr-3.3.0-1/lintr/tests/testthat/test-backport_linter.R | 20 lintr-3.3.0-1/lintr/tests/testthat/test-boolean_arithmetic_linter.R | 40 lintr-3.3.0-1/lintr/tests/testthat/test-brace_linter.R | 192 ++- lintr-3.3.0-1/lintr/tests/testthat/test-cache.R | 364 ------- lintr-3.3.0-1/lintr/tests/testthat/test-coalesce_linter.R |only lintr-3.3.0-1/lintr/tests/testthat/test-commented_code_linter.R | 30 lintr-3.3.0-1/lintr/tests/testthat/test-comparison_negation_linter.R | 21 lintr-3.3.0-1/lintr/tests/testthat/test-condition_call_linter.R | 20 lintr-3.3.0-1/lintr/tests/testthat/test-condition_message_linter.R | 71 - lintr-3.3.0-1/lintr/tests/testthat/test-conjunct_test_linter.R | 71 - lintr-3.3.0-1/lintr/tests/testthat/test-consecutive_assertion_linter.R | 12 lintr-3.3.0-1/lintr/tests/testthat/test-cyclocomp_linter.R | 32 lintr-3.3.0-1/lintr/tests/testthat/test-download_file_linter.R |only lintr-3.3.0-1/lintr/tests/testthat/test-empty_assignment_linter.R | 9 lintr-3.3.0-1/lintr/tests/testthat/test-exclusions.R | 45 lintr-3.3.0-1/lintr/tests/testthat/test-expect_comparison_linter.R | 19 lintr-3.3.0-1/lintr/tests/testthat/test-expect_lint.R | 44 lintr-3.3.0-1/lintr/tests/testthat/test-expect_true_false_linter.R | 29 lintr-3.3.0-1/lintr/tests/testthat/test-extraction_operator_linter.R | 37 lintr-3.3.0-1/lintr/tests/testthat/test-fixed_regex_linter.R | 141 +- lintr-3.3.0-1/lintr/tests/testthat/test-function_left_parentheses_linter.R | 61 - lintr-3.3.0-1/lintr/tests/testthat/test-get_source_expressions.R | 181 ++- lintr-3.3.0-1/lintr/tests/testthat/test-ids_with_token.R | 6 lintr-3.3.0-1/lintr/tests/testthat/test-if_switch_linter.R | 98 + lintr-3.3.0-1/lintr/tests/testthat/test-ifelse_censor_linter.R | 33 lintr-3.3.0-1/lintr/tests/testthat/test-implicit_assignment_linter.R | 165 +-- lintr-3.3.0-1/lintr/tests/testthat/test-implicit_integer_linter.R | 43 lintr-3.3.0-1/lintr/tests/testthat/test-indentation_linter.R | 221 ++-- lintr-3.3.0-1/lintr/tests/testthat/test-infix_spaces_linter.R | 73 - lintr-3.3.0-1/lintr/tests/testthat/test-is_numeric_linter.R | 26 lintr-3.3.0-1/lintr/tests/testthat/test-keyword_quote_linter.R | 54 - lintr-3.3.0-1/lintr/tests/testthat/test-length_test_linter.R | 100 +- lintr-3.3.0-1/lintr/tests/testthat/test-library_call_linter.R | 78 - lintr-3.3.0-1/lintr/tests/testthat/test-line_length_linter.R | 92 + lintr-3.3.0-1/lintr/tests/testthat/test-lint.R | 103 +- lintr-3.3.0-1/lintr/tests/testthat/test-lint_dir.R | 2 lintr-3.3.0-1/lintr/tests/testthat/test-lint_package.R | 6 lintr-3.3.0-1/lintr/tests/testthat/test-linter_tags.R | 69 + lintr-3.3.0-1/lintr/tests/testthat/test-list2df_linter.R |only lintr-3.3.0-1/lintr/tests/testthat/test-literal_coercion_linter.R | 74 + lintr-3.3.0-1/lintr/tests/testthat/test-make_linter_from_xpath.R | 59 + lintr-3.3.0-1/lintr/tests/testthat/test-matrix_apply_linter.R | 43 lintr-3.3.0-1/lintr/tests/testthat/test-methods.R | 22 lintr-3.3.0-1/lintr/tests/testthat/test-missing_argument_linter.R | 30 lintr-3.3.0-1/lintr/tests/testthat/test-namespace_linter.R | 36 lintr-3.3.0-1/lintr/tests/testthat/test-nzchar_linter.R | 43 lintr-3.3.0-1/lintr/tests/testthat/test-object_length_linter.R | 40 lintr-3.3.0-1/lintr/tests/testthat/test-object_name_linter.R | 252 +++-- lintr-3.3.0-1/lintr/tests/testthat/test-object_overwrite_linter.R | 4 lintr-3.3.0-1/lintr/tests/testthat/test-object_usage_linter.R | 228 ++-- lintr-3.3.0-1/lintr/tests/testthat/test-one_call_pipe_linter.R | 36 lintr-3.3.0-1/lintr/tests/testthat/test-outer_negation_linter.R | 34 lintr-3.3.0-1/lintr/tests/testthat/test-package_hooks_linter.R | 57 - lintr-3.3.0-1/lintr/tests/testthat/test-paste_linter.R | 123 +- lintr-3.3.0-1/lintr/tests/testthat/test-pipe_call_linter.R | 18 lintr-3.3.0-1/lintr/tests/testthat/test-pipe_consistency_linter.R | 129 +- lintr-3.3.0-1/lintr/tests/testthat/test-pipe_continuation_linter.R | 17 lintr-3.3.0-1/lintr/tests/testthat/test-pipe_return_linter.R | 6 lintr-3.3.0-1/lintr/tests/testthat/test-quotes_linter.R | 51 - lintr-3.3.0-1/lintr/tests/testthat/test-redundant_equals_linter.R | 17 lintr-3.3.0-1/lintr/tests/testthat/test-redundant_ifelse_linter.R | 46 lintr-3.3.0-1/lintr/tests/testthat/test-regex_subset_linter.R | 42 lintr-3.3.0-1/lintr/tests/testthat/test-return_linter.R | 289 +++-- lintr-3.3.0-1/lintr/tests/testthat/test-rstudio_markers.R | 2 lintr-3.3.0-1/lintr/tests/testthat/test-seq_linter.R | 67 + lintr-3.3.0-1/lintr/tests/testthat/test-settings.R | 92 - lintr-3.3.0-1/lintr/tests/testthat/test-sort_linter.R | 62 - lintr-3.3.0-1/lintr/tests/testthat/test-sprintf_linter.R | 81 + lintr-3.3.0-1/lintr/tests/testthat/test-string_boundary_linter.R | 79 + lintr-3.3.0-1/lintr/tests/testthat/test-strings_as_factors_linter.R | 38 lintr-3.3.0-1/lintr/tests/testthat/test-terminal_close_linter.R | 39 lintr-3.3.0-1/lintr/tests/testthat/test-todo_comment_linter.R | 38 lintr-3.3.0-1/lintr/tests/testthat/test-undesirable_function_linter.R | 59 - lintr-3.3.0-1/lintr/tests/testthat/test-undesirable_operator_linter.R | 67 - lintr-3.3.0-1/lintr/tests/testthat/test-unnecessary_concatenation_linter.R | 42 lintr-3.3.0-1/lintr/tests/testthat/test-unnecessary_lambda_linter.R | 137 +- lintr-3.3.0-1/lintr/tests/testthat/test-unnecessary_nested_if_linter.R | 260 ----- lintr-3.3.0-1/lintr/tests/testthat/test-unnecessary_nesting_linter.R | 223 ++-- lintr-3.3.0-1/lintr/tests/testthat/test-unnecessary_placeholder_linter.R | 24 lintr-3.3.0-1/lintr/tests/testthat/test-unneeded_concatenation_linter.R | 4 lintr-3.3.0-1/lintr/tests/testthat/test-unused_import_linter.R | 30 lintr-3.3.0-1/lintr/tests/testthat/test-use_lintr.R | 55 + lintr-3.3.0-1/lintr/tests/testthat/test-vector_logic_linter.R | 102 +- lintr-3.3.0-1/lintr/tests/testthat/test-which_grepl_linter.R | 2 lintr-3.3.0-1/lintr/tests/testthat/test-whitespace_linter.R | 26 lintr-3.3.0-1/lintr/tests/testthat/test-with.R | 21 lintr-3.3.0-1/lintr/tests/testthat/test-with_id.R | 9 lintr-3.3.0-1/lintr/tests/testthat/test-yoda_test_linter.R | 12 lintr-3.3.0-1/lintr/vignettes/lintr.Rmd | 9 258 files changed, 6142 insertions(+), 4505 deletions(-)