Title: Parametric and Non-Parametric Demographic Functions and
Applications
Description: Calculate parametric mortality and Fertility models, following packages 'BaSTA' in Colchero, Jones and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and 'BaFTA' <https://github.com/fercol/BaFTA>, summary statistics (e.g. ageing rates, life expectancy, lifespan equality, etc.), life table and product limit estimators from census data.
Author: Fernando Colchero [aut, cre]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Diff between paramDemo versions 1.0.2 dated 2025-01-16 and 1.0.3 dated 2026-10-13
DESCRIPTION | 12 ++-- MD5 | 10 +-- R/paramDemo.R | 126 +++++++++++++++++++++++++++++++++++++++++------ man/CalcLifeHist.Rd | 6 -- man/CalcMort.Rd | 9 +++ man/paramDemo-package.Rd | 4 - 6 files changed, 135 insertions(+), 32 deletions(-)
Title: Extra CRAN Submission Checks
Description: Provides automated checks for common Comprehensive R Archive
Network (CRAN) submission issues that are not caught by standard
'R CMD check'. Consolidates ad-hoc requirements that CRAN reviewers
enforce but standard checks do not surface, helping R package
maintainers identify and fix issues before submission to reduce
rejection rates. Covers code-pattern issues, DESCRIPTION-field
formatting, documentation problems, and general package structure
concerns.
Author: James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <james.balamuta@gmail.com>
Diff between checktor versions 0.1.0 dated 2026-07-02 and 0.2.0 dated 2026-10-13
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Title: Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Description: Calculates power for assessment of intermediate biomarker responses as correlates of risk in the active treatment group in clinical efficacy trials, as described in Gilbert, Janes, and Huang, Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials (2016, Statistics in Medicine). The methods differ from past approaches by accounting for the level of clinical treatment efficacy overall and in biomarker response subgroups, which enables the correlates of risk results to be interpreted in terms of potential correlates of efficacy/protection. The methods also account for inter-individual variability of the observed biomarker response that is not biologically relevant (e.g., due to technical measurement error of the laboratory assay used to measure the biomarker response), which is important because power to detect a specified correlate of risk effect size is heavily affected by the biomarker's measurement error. The methods can be used for a general binar [...truncated...]
Author: Stephanie Wu [aut],
Michal Juraska [aut, cre],
Peter Gilbert [aut],
Yunda Huang [aut],
Sebastien Haneuse [ctb, cph] code from
the osDesign package),
Takumi Saegusa [ctb, cph] code from the
osDesign package),
Nilanjan Chatterjee [ctb, cph] code fro [...truncated...]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between CoRpower versions 1.0.4 dated 2020-11-17 and 1.0.5 dated 2026-10-13
DESCRIPTION | 27 MD5 | 38 NAMESPACE | 7 NEWS.md |only R/computePower.R | 3686 ++++++++++---------- R/plotPowerCont.R | 396 +- R/plotPowerTri.R | 498 +- R/plotROCcurveTri.R | 336 - R/plotRRgradVE.R | 346 - R/tps.R |only build/vignette.rds |binary inst/doc/CoRpowerIntroduction.R | 588 +-- inst/doc/CoRpowerIntroduction.Rmd | 4 inst/doc/CoRpowerIntroduction.html | 2313 ++++++------ inst/doc/placeboAndBIPdataSimulationAlgorithms.html | 1005 ++--- man/computePower.Rd | 820 ++-- man/plotPowerCont.Rd | 202 - man/plotPowerTri.Rd | 182 man/plotROCcurveTri.Rd | 74 man/plotRRgradVE.Rd | 192 - vignettes/CoRpowerIntroduction.Rmd | 4 21 files changed, 5541 insertions(+), 5177 deletions(-)
Title: Building and Estimating Structural Equation Models
Description: A powerful, easy to use syntax for specifying and estimating complex
Structural Equation Models. Models can be estimated using Partial
Least Squares Path Modeling or Covariance-Based Structural Equation
Modeling or covariance based Confirmatory Factor Analysis (Ray, Danks, and Valdez 2021 <doi:10.2139/ssrn.3900621>).
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
Andre Calero Valdez [aut],
Juan Manuel Velasquez Estrada [ctb],
James Uanhoro [ctb],
Johannes Nakayama [ctb],
Lilian Koyan [ctb],
Laura Burbach [ctb],
Arturo Heynar Cano Bejar [ctb],
Susanne A [...truncated...]
Maintainer: Nicholas Patrick Danks <seminrgroup@gmail.com>
Diff between seminr versions 2.5.0 dated 2026-05-25 and 2.6.0 dated 2026-10-13
DESCRIPTION | 12 MD5 | 94 - NAMESPACE | 1 NEWS.md | 171 +++ R/compute_safe.R | 15 R/estimate_bootstrap.R | 86 + R/estimate_pls.R | 17 R/estimate_pls_mga.R | 7 R/estimate_simplePLS.R | 17 R/evaluate_effects.R | 6 R/evaluate_reliability.R | 2 R/evaluate_validity.R | 49 R/feature_cbsempredict.R |only R/feature_consistent.R | 151 ++ R/feature_plscpredict.R |only R/feature_plspredict.R | 558 ++++++---- R/helpers-mmMatrix.R | 5 R/helpers-model.R | 19 R/helpers-smMatrix.R | 13 R/library.R | 15 R/library_parallel.R | 50 R/plot_results.R | 18 R/report_summary.R | 7 inst/doc/SEMinR.R | 4 inst/doc/SEMinR.Rmd | 17 inst/doc/SEMinR.html | 51 man/PLSc.Rd | 11 man/bootstrap_model.Rd | 10 man/plot.reliability_table.Rd | 11 man/predict.cbsem_model.Rd |only man/predict.seminr_model.Rd | 23 man/predict_pls.Rd | 12 man/seminr-package.Rd | 2 tests/fixtures/V_3_6_0/composite_indicator_weights_p_values.csv | 10 tests/fixtures/V_3_6_0/composite_indicator_weights_t_values.csv | 10 tests/fixtures/V_3_6_0/factor_discriminant_validity_p_values.csv | 6 tests/fixtures/V_3_6_0/factor_discriminant_validity_t_values.csv | 6 tests/testthat/_snaps/plot-dot-snapshots.md | 24 tests/testthat/fixtures |only tests/testthat/test-accessors-mmMatrix.R | 34 tests/testthat/test-cbsempredict.R |only tests/testthat/test-consistent-interactions.R | 12 tests/testthat/test-consistent.R | 119 ++ tests/testthat/test-cran-core-limit.R |only tests/testthat/test-parallel-setup.R | 15 tests/testthat/test-plot-reliability.R |only tests/testthat/test-plsc-hoc.R |only tests/testthat/test-plscpredict.R |only tests/testthat/test-plspredict.R | 76 + tests/testthat/test-structure.r | 45 vignettes/SEMinR.Rmd | 17 51 files changed, 1462 insertions(+), 366 deletions(-)
Title: Flexible and Efficient Evaluation of Principal
Surrogates/Treatment Effect Modifiers
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB (2020), Inference on treatment effect modification by biomarker response in a three-phase sampling design, Biostatistics, 21(3): 545-560 <doi:10.1093/biostatistics/kxy074>. The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response ( [...truncated...]
Author: Michal Juraska [aut, cre],
Sebastien Haneuse [ctb, cph] code from
the osDesign package),
Takumi Saegusa [ctb, cph] code from the
osDesign package),
Nilanjan Chatterjee [ctb, cph] code from
the osDesign package),
Norman Breslow [ctb, cph] code fro [...truncated...]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between pssmooth versions 1.0.3 dated 2020-11-18 and 1.0.4 dated 2026-10-13
DESCRIPTION | 25 ++++++++++++++++--------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 - NEWS |binary R/pssmooth.R | 20 +++++++++++--------- R/tps.R |only build |only inst/CITATION | 19 +++++++------------ man/bootRiskCurve.Rd | 2 +- man/riskCurve.Rd | 6 +++--- man/summary.riskCurve.Rd | 2 +- man/testConstancy.Rd | 2 +- man/testEquality.Rd | 2 +- 13 files changed, 53 insertions(+), 48 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and its API borrows heavily from
the 'PyTorch' vision package.
Author: Tomasz Kalinowski [ctb, cre],
Daniel Falbel [aut, cph],
Christophe Regouby [ctb],
Akanksha Koshti [ctb],
Derrick Richard [ctb],
ANAMASGARD [ctb],
Chandraveer Singh [ctb],
Srishti Dutta [ctb],
Sebastian Fischer [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between torchvision versions 0.9.0 dated 2026-04-22 and 0.10.0 dated 2026-10-13
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torchvision-0.10.0/torchvision/tests/testthat/assets/class/aircraft |only torchvision-0.10.0/torchvision/tests/testthat/helper-torchvision.R | 114 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-biology.R | 4 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-damage.R | 4 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-doc.R | 2 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-infrared.R | 4 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-medical.R | 4 torchvision-0.10.0/torchvision/tests/testthat/test-collection-rf100-underwater.R | 4 torchvision-0.10.0/torchvision/tests/testthat/test-crop-geometry.R |only torchvision-0.10.0/torchvision/tests/testthat/test-dataset-caltech.R | 6 torchvision-0.10.0/torchvision/tests/testthat/test-dataset-cifar.R | 22 torchvision-0.10.0/torchvision/tests/testthat/test-dataset-cityscapes.R |only 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32 torchvision-0.10.0/torchvision/tests/testthat/test-models-inception.R | 44 torchvision-0.10.0/torchvision/tests/testthat/test-models-lw_detr.R |only torchvision-0.10.0/torchvision/tests/testthat/test-models-mask_rcnn.R | 76 torchvision-0.10.0/torchvision/tests/testthat/test-models-maxvit.R | 31 torchvision-0.10.0/torchvision/tests/testthat/test-models-rfdetr.R |only torchvision-0.10.0/torchvision/tests/testthat/test-models-vgg.R | 29 torchvision-0.10.0/torchvision/tests/testthat/test-models-vit.R | 23 torchvision-0.10.0/torchvision/tests/testthat/test-ops-box_convert.R | 77 torchvision-0.10.0/torchvision/tests/testthat/test-ops-boxes.R | 21 torchvision-0.10.0/torchvision/tests/testthat/test-target-transforms-detection.R |only torchvision-0.10.0/torchvision/tests/testthat/test-target-transforms-segmentation.R |only torchvision-0.10.0/torchvision/tests/testthat/test-transforms-array.R | 14 torchvision-0.10.0/torchvision/tests/testthat/test-transforms-defaults.R | 28 torchvision-0.10.0/torchvision/tests/testthat/test-transforms-magick.R | 21 torchvision-0.10.0/torchvision/tests/testthat/test-transforms-tensor.R | 248 +- torchvision-0.10.0/torchvision/tests/testthat/test-vision-utils.R | 327 ++ torchvision-0.10.0/torchvision/tools/convert-models.py | 44 torchvision-0.10.0/torchvision/vignettes/assets |only torchvision-0.10.0/torchvision/vignettes/torchvision-classes.Rmd |only torchvision-0.10.0/torchvision/vignettes/visualization-utilities.Rmd |only torchvision-0.9.0/torchvision/R/transforms-segmentation.R |only torchvision-0.9.0/torchvision/R/vision_utils.R |only torchvision-0.9.0/torchvision/tests/testthat/test-segmentation-transforms.R |only 232 files changed, 6729 insertions(+), 3942 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
Author: Michael Hahsler [aut, cre, cph] ,
John Forrest [aut, cph],
Matthew Bolanos [ctb],
Matthias Carnein [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.3-1 dated 2024-04-20 and 1.4.0 dated 2026-10-13
streamMOA-1.3-1/streamMOA/R/DSClassifier_MOA.R |only streamMOA-1.3-1/streamMOA/R/DSRegressor_MOA.R |only streamMOA-1.3-1/streamMOA/inst/doc/streamMOA.Rnw |only streamMOA-1.3-1/streamMOA/inst/doc/streamMOA.pdf |only streamMOA-1.3-1/streamMOA/man/DSClassifier_MOA.Rd |only streamMOA-1.3-1/streamMOA/man/DSRegressor_MOA.Rd |only streamMOA-1.3-1/streamMOA/vignettes/streamMOA.Rnw |only streamMOA-1.4.0/streamMOA/DESCRIPTION | 22 - streamMOA-1.4.0/streamMOA/MD5 | 87 ++--- streamMOA-1.4.0/streamMOA/NAMESPACE | 20 - streamMOA-1.4.0/streamMOA/NEWS.md | 8 streamMOA-1.4.0/streamMOA/R/DSC_BICO_MOA.R | 17 - streamMOA-1.4.0/streamMOA/R/DSC_CluStream.R | 15 streamMOA-1.4.0/streamMOA/R/DSC_ClusTree.R | 18 - streamMOA-1.4.0/streamMOA/R/DSC_DStream_MOA.R | 18 - streamMOA-1.4.0/streamMOA/R/DSC_DenStream.R | 47 +- streamMOA-1.4.0/streamMOA/R/DSC_MOA.R | 28 + streamMOA-1.4.0/streamMOA/R/DSC_streamkm.R | 41 +- streamMOA-1.4.0/streamMOA/R/DSD_MOA.R | 19 - streamMOA-1.4.0/streamMOA/R/DSD_RandomRBFGeneratorEvents.R | 50 +-- streamMOA-1.4.0/streamMOA/R/DSOutlier_MCOD.R | 55 --- streamMOA-1.4.0/streamMOA/R/ellipse.R | 2 streamMOA-1.4.0/streamMOA/README.md | 27 - streamMOA-1.4.0/streamMOA/build/partial.rdb |binary streamMOA-1.4.0/streamMOA/build/vignette.rds |binary streamMOA-1.4.0/streamMOA/inst/README_files/plot-1.png |binary streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.R | 164 +--------- streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.Rmd |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA.html |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.R |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.Rnw |only streamMOA-1.4.0/streamMOA/inst/doc/streamMOA_vignette.pdf |only streamMOA-1.4.0/streamMOA/java/README | 3 streamMOA-1.4.0/streamMOA/java/StreamMOA.java | 2 streamMOA-1.4.0/streamMOA/man/DSC_BICO_MOA.Rd | 36 +- streamMOA-1.4.0/streamMOA/man/DSC_CluStream.Rd | 31 - streamMOA-1.4.0/streamMOA/man/DSC_ClusTree.Rd | 34 +- streamMOA-1.4.0/streamMOA/man/DSC_DStream_MOA.Rd | 34 +- streamMOA-1.4.0/streamMOA/man/DSC_DenStream.Rd | 63 +-- streamMOA-1.4.0/streamMOA/man/DSC_MCOD.Rd | 47 +- streamMOA-1.4.0/streamMOA/man/DSC_MOA.Rd | 18 - streamMOA-1.4.0/streamMOA/man/DSC_StreamKM.Rd | 39 +- streamMOA-1.4.0/streamMOA/man/DSD_MOA.Rd | 23 - streamMOA-1.4.0/streamMOA/man/DSD_RandomRBFGeneratorEvents.Rd | 56 +-- streamMOA-1.4.0/streamMOA/man/figures/README-plot-1.png |only streamMOA-1.4.0/streamMOA/man/streamMOA-package.Rd | 7 streamMOA-1.4.0/streamMOA/tests |only streamMOA-1.4.0/streamMOA/vignettes/head.tex | 10 streamMOA-1.4.0/streamMOA/vignettes/streamMOA.Rmd |only streamMOA-1.4.0/streamMOA/vignettes/streamMOA_vignette.Rnw |only 50 files changed, 474 insertions(+), 567 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of the
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. It also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Author: Michael Hahsler [aut, cre, cph] ,
Margaret H. Dunham [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.2.1 dated 2024-04-21 and 1.2.3 dated 2026-10-13
rEMM-1.2.1/rEMM/inst/README_files |only rEMM-1.2.1/rEMM/inst/doc/rEMM.Rnw |only rEMM-1.2.1/rEMM/inst/doc/rEMM.pdf |only rEMM-1.2.1/rEMM/man/16S.Rd |only rEMM-1.2.1/rEMM/man/EMM.Rd |only rEMM-1.2.1/rEMM/vignettes/rEMM.Rnw |only rEMM-1.2.3/rEMM/DESCRIPTION | 27 - rEMM-1.2.3/rEMM/MD5 | 164 ++++--- rEMM-1.2.3/rEMM/NAMESPACE | 176 ++++--- rEMM-1.2.3/rEMM/NEWS.md | 20 rEMM-1.2.3/rEMM/R/AllClasses.R | 254 +++++++++++ rEMM-1.2.3/rEMM/R/AllGenerics.R | 80 +++ rEMM-1.2.3/rEMM/R/DSC_EMM.R | 85 +++ rEMM-1.2.3/rEMM/R/DSC_tNN.R | 2 rEMM-1.2.3/rEMM/R/EMM.R | 42 + rEMM-1.2.3/rEMM/R/SimpleMC.R | 5 rEMM-1.2.3/rEMM/R/TRAC.R | 32 + rEMM-1.2.3/rEMM/R/TRACDS.R | 6 rEMM-1.2.3/rEMM/R/build.R | 52 ++ rEMM-1.2.3/rEMM/R/cluster.R | 54 ++ rEMM-1.2.3/rEMM/R/combine.R | 37 + rEMM-1.2.3/rEMM/R/compact.R | 3 rEMM-1.2.3/rEMM/R/data.R |only rEMM-1.2.3/rEMM/R/fade.R | 61 ++ rEMM-1.2.3/rEMM/R/graph.R | 12 rEMM-1.2.3/rEMM/R/merge.R | 35 + rEMM-1.2.3/rEMM/R/object.size.R | 2 rEMM-1.2.3/rEMM/R/plot.R | 94 ++++ rEMM-1.2.3/rEMM/R/predict.R | 45 + rEMM-1.2.3/rEMM/R/prune.R | 54 ++ rEMM-1.2.3/rEMM/R/rEMM-package.R |only rEMM-1.2.3/rEMM/R/recluster.R | 87 +++ rEMM-1.2.3/rEMM/R/remove.R | 44 + rEMM-1.2.3/rEMM/R/reset.R | 2 rEMM-1.2.3/rEMM/R/score.R | 248 ++++++++++ rEMM-1.2.3/rEMM/R/smooth_transitions.R | 30 + rEMM-1.2.3/rEMM/R/synthetic_stream.R | 66 ++ rEMM-1.2.3/rEMM/R/tNN.R | 45 + rEMM-1.2.3/rEMM/R/transition.R | 91 ++++ rEMM-1.2.3/rEMM/R/update.R | 52 ++ rEMM-1.2.3/rEMM/README.md | 129 +++-- rEMM-1.2.3/rEMM/build/partial.rdb |binary rEMM-1.2.3/rEMM/build/vignette.rds |binary rEMM-1.2.3/rEMM/inst/doc/TRAC.R |only rEMM-1.2.3/rEMM/inst/doc/TRAC.Rmd |only rEMM-1.2.3/rEMM/inst/doc/TRAC.html |only rEMM-1.2.3/rEMM/inst/doc/rEMM.R | 385 ++--------------- rEMM-1.2.3/rEMM/inst/doc/rEMM.Rmd |only rEMM-1.2.3/rEMM/inst/doc/rEMM.html |only rEMM-1.2.3/rEMM/inst/doc/rEMM_paper_vignette.R |only rEMM-1.2.3/rEMM/inst/doc/rEMM_paper_vignette.Rnw |only rEMM-1.2.3/rEMM/inst/doc/rEMM_paper_vignette.pdf |only rEMM-1.2.3/rEMM/inst/doc/stream.R |only rEMM-1.2.3/rEMM/inst/doc/stream.Rmd |only rEMM-1.2.3/rEMM/inst/doc/stream.html |only rEMM-1.2.3/rEMM/man/DSC_EMM.Rd | 94 ++-- rEMM-1.2.3/rEMM/man/Derwent.Rd | 43 - rEMM-1.2.3/rEMM/man/EMM-class.Rd | 171 ++++--- rEMM-1.2.3/rEMM/man/EMMTraffic.Rd | 30 - rEMM-1.2.3/rEMM/man/EMMsim.Rd | 31 - rEMM-1.2.3/rEMM/man/TRAC-class.Rd | 33 - rEMM-1.2.3/rEMM/man/TRACDS-class.Rd | 81 ++- rEMM-1.2.3/rEMM/man/build.Rd | 52 +- rEMM-1.2.3/rEMM/man/cluster.Rd | 55 +- rEMM-1.2.3/rEMM/man/combine.Rd | 37 - rEMM-1.2.3/rEMM/man/fade.Rd | 47 +- rEMM-1.2.3/rEMM/man/figures/README-example_data-1.png |only rEMM-1.2.3/rEMM/man/figures/README-example_model-1.png |only rEMM-1.2.3/rEMM/man/find_clusters.Rd | 49 +- rEMM-1.2.3/rEMM/man/merge.Rd | 53 +- rEMM-1.2.3/rEMM/man/plot.EMM.Rd | 50 +- rEMM-1.2.3/rEMM/man/predict.Rd | 72 +-- rEMM-1.2.3/rEMM/man/prune.Rd | 68 +-- rEMM-1.2.3/rEMM/man/rEMM-package.Rd |only rEMM-1.2.3/rEMM/man/rRNA16S.Rd |only rEMM-1.2.3/rEMM/man/recluster.Rd | 111 ++-- rEMM-1.2.3/rEMM/man/remove.Rd | 37 - rEMM-1.2.3/rEMM/man/score.Rd | 108 ++-- rEMM-1.2.3/rEMM/man/smooth_transitions.Rd | 30 - rEMM-1.2.3/rEMM/man/synthetic_stream.Rd | 81 ++- rEMM-1.2.3/rEMM/man/tNN-class.Rd | 86 ++- rEMM-1.2.3/rEMM/man/transition.Rd | 81 ++- rEMM-1.2.3/rEMM/man/transition_table.Rd | 68 +-- rEMM-1.2.3/rEMM/man/update.Rd | 56 +- rEMM-1.2.3/rEMM/tests/testthat.R | 4 rEMM-1.2.3/rEMM/tests/testthat/helper-models.R |only rEMM-1.2.3/rEMM/tests/testthat/test-EMM.R | 181 +++++-- rEMM-1.2.3/rEMM/tests/testthat/test-clustering.R |only rEMM-1.2.3/rEMM/tests/testthat/test-interfaces.R |only rEMM-1.2.3/rEMM/tests/testthat/test-recluster-fade.R |only rEMM-1.2.3/rEMM/tests/testthat/test-remove.R | 161 +++++-- rEMM-1.2.3/rEMM/tests/testthat/test-score-predict.R |only rEMM-1.2.3/rEMM/tests/testthat/test-transitions.R |only rEMM-1.2.3/rEMM/vignettes/TRAC.Rmd |only rEMM-1.2.3/rEMM/vignettes/misc.bib | 4 rEMM-1.2.3/rEMM/vignettes/rEMM.Rmd |only rEMM-1.2.3/rEMM/vignettes/rEMM.bib | 36 + rEMM-1.2.3/rEMM/vignettes/rEMM_paper_vignette.Rnw |only rEMM-1.2.3/rEMM/vignettes/stream.Rmd |only 99 files changed, 3150 insertions(+), 1381 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.1.3 dated 2026-07-21 and 0.1.4 dated 2026-10-13
ChangeLog | 78 +++++++ DESCRIPTION | 8 MD5 | 83 ++++---- R/RcppExports.R | 4 R/calendars.R | 8 R/dates.R | 2 README.md | 6 build/partial.rdb |binary configure | 2 inst/NEWS.Rd | 13 + man/advanceUnits.Rd | 2 man/getCalendar.Rd | 2 man/getName.Rd | 2 src/Makevars.in | 2 src/Makevars.win.in | 2 src/calendars.cpp | 65 ++++-- src/ql/optional.hpp | 34 +-- src/ql/patterns/observable.cpp | 53 +++-- src/ql/settings.cpp | 19 + src/ql/settings.hpp | 25 -- src/ql/time/calendars/all.hpp | 2 src/ql/time/calendars/argentina.hpp | 2 src/ql/time/calendars/bespokecalendar.hpp | 2 src/ql/time/calendars/hongkong.cpp | 15 + src/ql/time/calendars/indonesia.cpp | 311 +++++++++++++++++++++++++++++- src/ql/time/calendars/italy.cpp | 4 src/ql/time/calendars/italy.hpp | 27 -- src/ql/time/calendars/malaysia.cpp |only src/ql/time/calendars/malaysia.hpp |only src/ql/time/calendars/philippines.cpp |only src/ql/time/calendars/philippines.hpp |only src/ql/time/calendars/saudiarabia.cpp | 161 ++++++++------- src/ql/time/calendars/saudiarabia.hpp | 12 - src/ql/time/calendars/singapore.cpp | 16 + src/ql/time/calendars/singapore.hpp | 2 src/ql/time/calendars/southafrica.cpp | 11 - src/ql/time/calendars/sweden.hpp | 2 src/ql/time/calendars/thailand.cpp | 6 src/ql/time/calendars/thailand.hpp | 4 src/ql/time/calendars/turkey.cpp | 2 src/ql/time/date.cpp | 38 +++ src/ql/time/period.cpp | 7 src/ql/utilities/null.hpp | 44 +--- src/ql/utilities/null_deleter.hpp |only src/xptr.cpp | 4 45 files changed, 804 insertions(+), 278 deletions(-)
Title: Regularized Point Processes and Stochastic Marginalization for
Extremes
Description: Implements a non-stationary extreme value analysis framework
by coupling a covariate-driven non-homogeneous Poisson process (NHPP)
with (adaptive) elastic-net regularization and analytical gradients.
Provides methods for estimating conditional return levels and
unconditional (marginalized) return levels via parametric stochastic
integration over stable vector autoregressive VAR(p) covariate
trajectories, or non-parametric annual-block resampling. Supports
block-specific penalty controls, BIC selection along a regularization
path, Karush-Kuhn-Tucker convergence checks, time-rescaling residual
diagnostics, conditional parametric bootstrap inference, and
walk-forward assessment.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between margEVT versions 0.3.0 dated 2026-09-23 and 0.4.0 dated 2026-10-13
margEVT-0.3.0/margEVT/man/dot-select_lambda_bic.Rd |only margEVT-0.4.0/margEVT/DESCRIPTION | 27 margEVT-0.4.0/margEVT/MD5 | 100 - margEVT-0.4.0/margEVT/NAMESPACE | 8 margEVT-0.4.0/margEVT/NEWS.md | 78 margEVT-0.4.0/margEVT/R/backtest.R | 179 +- margEVT-0.4.0/margEVT/R/bootstrap.R | 729 ++++---- margEVT-0.4.0/margEVT/R/covariate.R | 459 +++-- margEVT-0.4.0/margEVT/R/design.R | 8 margEVT-0.4.0/margEVT/R/fit.R | 1104 +++++++------ margEVT-0.4.0/margEVT/R/generator.R | 492 +++-- margEVT-0.4.0/margEVT/R/likelihood.R | 521 +++--- margEVT-0.4.0/margEVT/R/marginalize.R | 764 +++++--- margEVT-0.4.0/margEVT/R/methods.R |only margEVT-0.4.0/margEVT/R/params.R | 8 margEVT-0.4.0/margEVT/R/select.R | 438 ++--- margEVT-0.4.0/margEVT/R/utils.R | 531 ++---- margEVT-0.4.0/margEVT/build |only margEVT-0.4.0/margEVT/inst/CITATION | 44 margEVT-0.4.0/margEVT/inst/doc |only margEVT-0.4.0/margEVT/man/active_covariates.Rd | 14 margEVT-0.4.0/margEVT/man/backtest.Rd | 42 margEVT-0.4.0/margEVT/man/bic_nhpp.Rd | 13 margEVT-0.4.0/margEVT/man/bootstrap_coef.Rd | 39 margEVT-0.4.0/margEVT/man/bootstrap_rl.Rd | 41 margEVT-0.4.0/margEVT/man/build_cov_annual.Rd | 21 margEVT-0.4.0/margEVT/man/build_design_matrices.Rd | 9 margEVT-0.4.0/margEVT/man/coef.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/fit_nhpp.Rd | 92 - margEVT-0.4.0/margEVT/man/fit_var_generator.Rd | 92 - margEVT-0.4.0/margEVT/man/is_nhpp_fit.Rd | 3 margEVT-0.4.0/margEVT/man/marginalize.Rd | 61 margEVT-0.4.0/margEVT/man/n_exceedances.Rd | 10 margEVT-0.4.0/margEVT/man/nhpp_fit-methods.Rd |only margEVT-0.4.0/margEVT/man/plot.nhpp_fit.Rd | 38 margEVT-0.4.0/margEVT/man/plot.nhpp_rl.Rd |only margEVT-0.4.0/margEVT/man/pp_grad.Rd | 20 margEVT-0.4.0/margEVT/man/pp_nllh.Rd | 29 margEVT-0.4.0/margEVT/man/predict_params.Rd | 9 margEVT-0.4.0/margEVT/man/print.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/print.summary.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/residuals.nhpp_fit.Rd |only margEVT-0.4.0/margEVT/man/rl_table.Rd | 9 margEVT-0.4.0/margEVT/man/seasonal_harmonics.Rd |only margEVT-0.4.0/margEVT/man/simulate_covariates.Rd | 33 margEVT-0.4.0/margEVT/man/summary.nhpp_fit.Rd | 21 margEVT-0.4.0/margEVT/tests/testthat/test-bootstrap-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-bootstrap.R | 4 margEVT-0.4.0/margEVT/tests/testthat/test-covariate.R | 15 margEVT-0.4.0/margEVT/tests/testthat/test-estimation-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-fit.R | 8 margEVT-0.4.0/margEVT/tests/testthat/test-generator-v04.R |only margEVT-0.4.0/margEVT/tests/testthat/test-generator.R | 43 margEVT-0.4.0/margEVT/tests/testthat/test-marginalize.R | 81 margEVT-0.4.0/margEVT/tests/testthat/test-methods.R |only margEVT-0.4.0/margEVT/tests/testthat/test-select.R | 56 margEVT-0.4.0/margEVT/tests/testthat/test-utils.R | 14 margEVT-0.4.0/margEVT/vignettes |only 58 files changed, 3872 insertions(+), 2435 deletions(-)
Title: Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq
Data
Description: A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>).
Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any
type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),
TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends
standard NR-seq standard NR-seq mutational modeling to support multi-label analyses
(e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better
account for transcript-to-transcript variance in metabolic label incorporation.
'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses
of premature mRNA processing and flow between subcellular compartments. Finally,
'EZbakR' implements flexible and well-powered comparative analyses of all
estimated parameters via design matrix-specified generalized linear modeling.
Author: Isaac Vock [aut, cre, cph]
Maintainer: Isaac Vock <isaac.vock@gmail.com>
Diff between EZbakR versions 0.1.0 dated 2025-12-10 and 0.2.2 dated 2026-10-13
DESCRIPTION | 9 LICENSE | 4 MD5 | 151 NEWS.md | 28 R/Comparisons.R | 2915 +++++++++--------- R/Dropout.R | 1932 ++++++------ R/EZbakRArrowData.R | 856 ++--- R/EZbakRData.R | 814 ++--- R/EZbakRFractions.R | 905 ++--- R/EZbakRKinetics.R | 775 ++-- R/Fractions.R | 5524 +++++++++++++++++----------------- R/Helpers.R | 2740 ++++++++--------- R/Isoforms.R | 2396 +++++++-------- R/Kinetics.R | 1988 ++++++------ R/ODEs.R | 3577 +++++++++++----------- R/QC.R | 2748 ++++++++--------- R/Simulations.R | 6166 +++++++++++++++++++-------------------- R/Visualizations.R | 1902 ++++++------ R/data.R | 204 - R/simple-functions.R | 482 +-- README.md | 148 build/partial.rdb |only build/vignette.rds |binary inst/doc/EZDynamics.R | 53 inst/doc/EZDynamics.Rmd | 1695 +++++----- inst/doc/EZDynamics.html | 628 ++- inst/doc/EZQC.Rmd | 274 - inst/doc/EZQC.html | 176 - inst/doc/EZget.html | 65 inst/doc/EstimateFractions.Rmd | 1260 +++---- inst/doc/EstimateFractions.html | 30 inst/doc/EstimateKinetics.Rmd | 4 inst/doc/EstimateKinetics.html | 15 inst/doc/Linear-modeling.Rmd | 1094 +++--- inst/doc/Linear-modeling.html | 13 inst/doc/Quickstart.html | 15 man/CompareParameters.Rd | 3 man/CorrectDropout.Rd | 8 man/DeconvolveFractions.Rd | 296 - man/EZDynamics.Rd | 5 man/EZQC.EZbakRArrowData.Rd | 86 man/EZQC.Rd | 2 man/EZSimulate.Rd | 9 man/EZbakRArrowData.Rd | 270 - man/EZbakRData.Rd | 238 - man/EZbakRFractions.Rd | 3 man/EZbakRKinetics.Rd | 3 man/EZpcaPlot.Rd | 186 - man/EstimateFractions.Rd | 2 man/EstimateIsoformFractions.Rd | 2 man/EstimateMutRates.Rd | 210 - man/ImportIsoformQuant.Rd | 166 - man/NormalizeForDropout.Rd | 238 - man/SimpleSim.Rd | 92 man/SimulateIsoforms.Rd | 192 - man/SimulateMultiCondition.Rd | 398 +- man/SimulateOneRep.Rd | 254 - man/create_fraction_design.Rd | 98 man/example_cB.Rd | 68 man/example_metadf.Rd | 56 man/new_EZbakRArrowData.Rd | 38 man/new_EZbakRData.Rd | 38 man/print.EZbakRArrowData.Rd | 68 man/print.EZbakRData.Rd | 68 man/standard_fraction_design.Rd | 52 man/tilac_fraction_design.Rd | 66 man/validate_EZbakRArrowData.Rd | 30 man/validate_EZbakRData.Rd | 30 man/validate_EZbakRFractions.Rd | 30 tests/testthat.R | 24 tests/testthat/test-EZbakRData.R | 282 - tests/testthat/test-SimpleSim.R | 10 vignettes/EZDynamics.Rmd | 1695 +++++----- vignettes/EZQC.Rmd | 274 - vignettes/EstimateFractions.Rmd | 1260 +++---- vignettes/EstimateKinetics.Rmd | 4 vignettes/Linear-modeling.Rmd | 1094 +++--- 77 files changed, 24975 insertions(+), 24559 deletions(-)
Title: Bias and Uncertainty Corrected Sample Size
Description: Implements sample size planning for a future study from the summary
statistics of a prior study, correcting the prior effect for publication bias
and uncertainty so the planned study attains its target statistical power more
reliably than methods that take a sample effect size at face value. Planners
cover the one-sample, paired, independent, and Welch t tests; between-subjects
analysis of variance and covariance; within-subjects and split-plot analysis
of variance; a regression coefficient, the squared multiple correlation, and a
subset of predictors; the Pearson correlation; a two-group multivariate
comparison; and the chi square difference between nested models. The
regression planners can treat the predictors as fixed or as sampled, the
within-subjects and split-plot planners accept a sphericity correction, and
each plan reports the effect size it is built on. A simulation function
audits how often a plan attains its target power. The method is described in
Anderson, Kelley, and Ma [...truncated...]
Author: Ken Kelley [aut, cre] ,
Samantha F. Anderson [aut] ,
Scott E. Maxwell [aut]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between BUCSS versions 1.2.1 dated 2020-08-25 and 2.0.0 dated 2026-10-13
BUCSS-1.2.1/BUCSS/R/ss.power.ba.R |only BUCSS-1.2.1/BUCSS/R/ss.power.ba.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.dt.r |only BUCSS-1.2.1/BUCSS/R/ss.power.it.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg.all.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg.joint.R |only BUCSS-1.2.1/BUCSS/R/ss.power.reg1.R |only BUCSS-1.2.1/BUCSS/R/ss.power.spa.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.spa.r |only BUCSS-1.2.1/BUCSS/R/ss.power.wa.general.R |only BUCSS-1.2.1/BUCSS/R/ss.power.wa.r |only BUCSS-1.2.1/BUCSS/man/ss.power.ba.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.ba.general.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.dt.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.it.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg.all.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg.joint.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.reg1.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.spa.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.spa.general.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.wa.Rd |only BUCSS-1.2.1/BUCSS/man/ss.power.wa.general.Rd |only BUCSS-2.0.0/BUCSS/DESCRIPTION | 55 +- BUCSS-2.0.0/BUCSS/MD5 | 137 ++++- BUCSS-2.0.0/BUCSS/NAMESPACE | 69 ++- BUCSS-2.0.0/BUCSS/NEWS.md |only BUCSS-2.0.0/BUCSS/R/BUCSS.R | 178 +++++++ BUCSS-2.0.0/BUCSS/R/bucss-broom.R |only BUCSS-2.0.0/BUCSS/R/bucss-design-registry.R |only BUCSS-2.0.0/BUCSS/R/bucss-internal.R |only BUCSS-2.0.0/BUCSS/R/bucss-output-helpers.R |only BUCSS-2.0.0/BUCSS/R/bucss-plot.R |only BUCSS-2.0.0/BUCSS/R/bucss-sensitivity.R |only BUCSS-2.0.0/BUCSS/R/legacy.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_R2.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_ancova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_chisq_diff.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_correlation.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_factorial_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_factorial_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_independent_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_manova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_mixed_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_mixed_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_one_sample_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_one_way_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_paired_t.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_reg_coef.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_reg_joint.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_rm_anova.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_rm_anova_general.R |only BUCSS-2.0.0/BUCSS/R/ss_buc_welch_t.R |only BUCSS-2.0.0/BUCSS/README.md | 367 +++++++++++++++- BUCSS-2.0.0/BUCSS/build |only BUCSS-2.0.0/BUCSS/inst |only BUCSS-2.0.0/BUCSS/man/BUCSS-package.Rd | 164 ++++++- BUCSS-2.0.0/BUCSS/man/bucss-deprecated.Rd |only BUCSS-2.0.0/BUCSS/man/bucss_tidiers.Rd |only BUCSS-2.0.0/BUCSS/man/figures |only BUCSS-2.0.0/BUCSS/man/planning_sentence.Rd |only BUCSS-2.0.0/BUCSS/man/plot.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/print.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/print.bucss_sensitivity.Rd |only BUCSS-2.0.0/BUCSS/man/reexports.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_R2.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_ancova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_chisq_diff.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_correlation.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_factorial_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_factorial_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_independent_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_manova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_mixed_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_mixed_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_one_sample_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_one_way_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_paired_t.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_reg_coef.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_reg_joint.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_rm_anova.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_rm_anova_general.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_sensitivity.Rd |only BUCSS-2.0.0/BUCSS/man/ss_buc_welch_t.Rd |only BUCSS-2.0.0/BUCSS/man/sub-.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/man/sub-sub-.bucss_plan.Rd |only BUCSS-2.0.0/BUCSS/tests |only BUCSS-2.0.0/BUCSS/vignettes |only 87 files changed, 905 insertions(+), 65 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut, cre]
Maintainer: Synthesize Bio <candace@synthesize.bio>
Diff between rsynthbio versions 4.2.0 dated 2026-06-12 and 4.2.1 dated 2026-10-13
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++------- NEWS.md | 7 ++++ R/call_model_api.R | 45 +++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/baseline.R | 2 - inst/doc/baseline.Rmd | 2 - inst/doc/getting-started.R | 2 - inst/doc/getting-started.Rmd | 2 - tests/testthat/fixtures |only tests/testthat/test-validation-errors.R |only vignettes/baseline.Rmd | 2 - vignettes/getting-started.Rmd | 2 - 13 files changed, 69 insertions(+), 23 deletions(-)
Title: 'rmarkdown' Extension for Formatted 'RJDemetra' Outputs
Description: Functions to have nice 'rmarkdown' outputs of the
seasonal and trading day adjustment models made with 'RJDemetra'.
Author: Alain Quartier-la-Tente [aut, cre, cph]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjdmarkdown versions 0.2.2 dated 2023-10-04 and 0.2.3 dated 2026-10-13
DESCRIPTION | 17 ++--- MD5 | 20 +++--- NAMESPACE | 20 ++++-- NEWS.md | 5 + R/print_preprocessing.R | 2 README.md | 10 +-- build/vignette.rds |binary inst/doc/rjdmarkdown-html.R | 114 ++++++++++++++++++------------------- inst/doc/rjdmarkdown-html.html | 7 +- inst/doc/rjdmarkdown-pdf.R | 126 ++++++++++++++++++++--------------------- inst/doc/rjdmarkdown-pdf.pdf |binary 11 files changed, 167 insertions(+), 154 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet,
NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Author: Eduard Szoecs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmueller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
Joao Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Ethan Bass [ctb],
Tamas Stirling [ctb, cre [...truncated...]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.3.1 dated 2025-07-16 and 2.0.0 dated 2026-10-13
DESCRIPTION | 27 MD5 | 134 ++-- NAMESPACE | 77 +- NEWS.md | 27 R/bcpc.R | 31 - R/chebi.R | 21 R/chembl.R | 1045 ++++++++++++++++++++++++++++++++-- R/chembl_offline.R |only R/chemspider.R | 27 R/cir.R | 12 R/cts.R | 4 R/etox.R | 24 R/eup.R |only R/foodb.R |only R/onLoad.R |only R/pubchem.R | 553 +++++------------ R/pubchem_pugview.R |only R/utils.R | 83 ++ R/zzz.R | 4 build/vignette.rds |binary inst/doc/pubchem-pages.Rmd |only inst/doc/pubchem-pages.html |only inst/doc/webchem-offline.Rmd |only inst/doc/webchem-offline.html |only inst/doc/webchem.html | 5 man/bcpc_query.Rd | 2 man/chebi_comp_entity.Rd | 7 man/chembl_atc_classes.Rd | 4 man/chembl_check_db_version.Rd |only man/chembl_img.Rd |only man/chembl_query.Rd | 150 ++++ man/chembl_status.Rd |only man/cir_img.Rd | 3 man/cir_query.Rd | 9 man/cs_check_key.Rd | 6 man/cs_compinfo.Rd | 5 man/cs_convert.Rd | 5 man/cs_datasources.Rd | 5 man/cs_extcompinfo.Rd | 8 man/cts_from.Rd | 2 man/cts_to.Rd | 2 man/db_connect.Rd |only man/db_download_chembl.Rd |only man/db_download_eup.Rd |only man/db_download_foodb.Rd |only man/etox_basic.Rd | 5 man/etox_targets.Rd | 5 man/etox_tests.Rd | 5 man/eup_convert.Rd |only man/eup_list_entries.Rd |only man/eup_query.Rd |only man/foodb_convert.Rd |only man/foodb_list_compounds.Rd |only man/foodb_query.Rd |only man/get_chebiid.Rd | 9 man/get_cid.Rd | 8 man/get_csid.Rd | 5 man/get_etoxid.Rd | 5 man/pc_sect.Rd | 6 man/webchem-package.Rd | 3 tests/testthat/test-bcpc.R | 13 tests/testthat/test-chebi.R | 7 tests/testthat/test-chembl.R | 262 +++++++- tests/testthat/test-chembl_offline.R |only tests/testthat/test-cir.R | 7 tests/testthat/test-cts.R | 15 tests/testthat/test-etox.R | 380 ++++++------ tests/testthat/test-eup.R |only tests/testthat/test-extractors.R | 34 - tests/testthat/test-flavornet.R | 8 tests/testthat/test-foodb.R |only tests/testthat/test-integration.R | 12 tests/testthat/test-nist.R | 34 + tests/testthat/test-opsin.R | 4 tests/testthat/test-pubchem-pugview.R |only tests/testthat/test-pubchem.R | 45 - tests/testthat/test-srs.R | 3 tests/testthat/test-utils.R | 26 tests/testthat/test-wikidata.R | 7 vignettes/precompile.R | 2 vignettes/pubchem-pages.Rmd |only vignettes/webchem-offline.Rmd |only 82 files changed, 2280 insertions(+), 912 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.4-6 dated 2026-10-01 and 1.4-7 dated 2026-10-13
DESCRIPTION | 12 ++--- MD5 | 25 ++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/NAMI.R | 101 ++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/NAMI.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++++-- inst/doc/NAMI.pdf |binary inst/doc/mtram.pdf |binary inst/doc/survtram.pdf |binary inst/doc/tram.pdf |binary tests/Polr-Ex.Rout.save |only tests/bugfixes.R | 15 ++++--- vignettes/NAMI.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++++-- 14 files changed, 330 insertions(+), 33 deletions(-)
Title: Modeling Data with Functional Programming
Description: A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Author: Brian Lee Yung Rowe [aut, cre]
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between lambda.r versions 1.2.4 dated 2019-09-18 and 1.2.6 dated 2026-10-13
DESCRIPTION | 16 +++++++++++----- MD5 | 4 ++-- man/lambda.r-package.Rd | 7 ++++--- 3 files changed, 17 insertions(+), 10 deletions(-)
Title: Cluster Origin-Destination Flow Data
Description: Provides functionality for clustering
origin-destination (OD) pairs, representing desire lines (or flows).
This includes creating distance matrices between OD pairs and passing
distance matrices to a clustering algorithm. See the academic paper
Tao and Thill (2016) <doi:10.1111/gean.12100>
for more details on spatial clustering of flows.
See the paper on delineating demand-responsive operating areas
by Mahfouz et al. (2025) <doi:10.1016/j.urbmob.2025.100135>
for an example of how this package can be used to cluster flows for
applied transportation research.
Author: Hussein Mahfouz [aut, cre] ,
Robin Lovelace [aut]
Maintainer: Hussein Mahfouz <husseinmahfouz93@gmail.com>
Diff between flowcluster versions 0.2.1 dated 2025-08-21 and 0.2.2 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/testthat/test-clustering.R | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get star [...truncated...]
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
Rider Johnson [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 17.3 dated 2026-05-05 and 18.0 dated 2026-10-13
fields-17.3/fields/R/BD.R |only fields-17.3/fields/R/ChicagoO3.R |only fields-17.3/fields/R/RMprecip.R |only fields-17.3/fields/R/flame.R |only fields-17.3/fields/R/imagePlotOLD.R |only fields-17.3/fields/R/minitri.R |only fields-17.3/fields/R/panelPlotExample.R |only fields-17.3/fields/R/rat.diet.R |only fields-17.3/fields/R/setupLegend.R |only fields-17.3/fields/tests/cmdfile |only fields-18.0/fields/DESCRIPTION | 8 fields-18.0/fields/LICENSE.note | 2 fields-18.0/fields/MD5 | 711 +++++++------- fields-18.0/fields/NAMESPACE | 5 fields-18.0/fields/R/Exponential.R | 4 fields-18.0/fields/R/ExponentialUpper.R | 4 fields-18.0/fields/R/Krig.R | 34 fields-18.0/fields/R/Krig.family.R | 52 - fields-18.0/fields/R/KrigFindLambda.R | 14 fields-18.0/fields/R/Matern.R | 2 fields-18.0/fields/R/Matern.parameters.R | 4 fields-18.0/fields/R/Paciorek.cov.R | 2 fields-18.0/fields/R/QSreg.R | 6 fields-18.0/fields/R/QTps.R | 6 fields-18.0/fields/R/RadialBasis.R | 2 fields-18.0/fields/R/RdistEarth.R | 2 fields-18.0/fields/R/SUBSCRIPTINGSpatialDesign.R | 2 fields-18.0/fields/R/Tps.R | 2 fields-18.0/fields/R/Tps.cov.R | 27 fields-18.0/fields/R/US.R | 2 fields-18.0/fields/R/add.image.R | 4 fields-18.0/fields/R/addColorBar.R |only fields-18.0/fields/R/addColorBarTriangle.R | 2 fields-18.0/fields/R/addLegend.R | 36 fields-18.0/fields/R/addTitleBox.R |only fields-18.0/fields/R/approximateCovariance2D.R | 17 fields-18.0/fields/R/arrow.plot.R | 3 fields-18.0/fields/R/as.image.R | 2 fields-18.0/fields/R/as.surface.R | 2 fields-18.0/fields/R/augmentPredictionGrid.R | 21 fields-18.0/fields/R/bisection.search.R | 2 fields-18.0/fields/R/bplot.family.R | 35 fields-18.0/fields/R/bubblePlot.R | 95 + fields-18.0/fields/R/cat.matrix.R | 2 fields-18.0/fields/R/cat.to.list.R | 2 fields-18.0/fields/R/ceiling2.R | 2 fields-18.0/fields/R/circulantEmbedding.R | 4 fields-18.0/fields/R/circulantEmbeddingSetup.R | 2 fields-18.0/fields/R/coef.Krig.R | 2 fields-18.0/fields/R/color.scale.R | 4 fields-18.0/fields/R/colorBar.R | 4 fields-18.0/fields/R/colorbar.plot.R | 6 fields-18.0/fields/R/compactToMat.R | 6 fields-18.0/fields/R/confidenceIntervalMLE.R | 2 fields-18.0/fields/R/cover.design.R | 8 fields-18.0/fields/R/cubic.cov.R | 4 fields-18.0/fields/R/describe.R | 2 fields-18.0/fields/R/discretize.image.R | 2 fields-18.0/fields/R/divMap.R | 21 fields-18.0/fields/R/double.exp.R | 2 fields-18.0/fields/R/drape.color.R | 6 fields-18.0/fields/R/drape.plot.R | 2 fields-18.0/fields/R/dyadic.2check.R | 2 fields-18.0/fields/R/dyadic.check.R | 2 fields-18.0/fields/R/ensembleEnvelope.R |only fields-18.0/fields/R/envelopePlot.R | 15 fields-18.0/fields/R/evlpoly.R | 2 fields-18.0/fields/R/evlpoly2.R | 2 fields-18.0/fields/R/exp.cov.R | 4 fields-18.0/fields/R/exp.earth.cov.R | 4 fields-18.0/fields/R/exp.image.cov.R | 2 fields-18.0/fields/R/exp.simple.cov.R | 8 fields-18.0/fields/R/fast.1way.R | 2 fields-18.0/fields/R/fastTps.R | 4 fields-18.0/fields/R/fields.color.picker.R | 2 fields-18.0/fields/R/fields.convert.grid.R | 2 fields-18.0/fields/R/fields.derivative.poly.R | 2 fields-18.0/fields/R/fields.duplicated.matrix.R | 2 fields-18.0/fields/R/fields.mkpoly.R | 4 fields-18.0/fields/R/fields.rdist.near.R | 2 fields-18.0/fields/R/fields.style.R | 2 fields-18.0/fields/R/fields.x.to.grid.R | 4 fields-18.0/fields/R/fillGrid.R | 21 fields-18.0/fields/R/find.upcross.R | 2 fields-18.0/fields/R/findGridBox.R | 2 fields-18.0/fields/R/fitted.Krig.R | 2 fields-18.0/fields/R/gauss.cov.R | 2 fields-18.0/fields/R/gcv.sreg.R | 8 fields-18.0/fields/R/golden.section.search.R | 4 fields-18.0/fields/R/image.family.R | 6 fields-18.0/fields/R/image.plot.R | 4 fields-18.0/fields/R/image.smooth.R | 12 fields-18.0/fields/R/imagePlot.R | 15 fields-18.0/fields/R/in.poly.R | 2 fields-18.0/fields/R/interp.surface.FFT.R | 21 fields-18.0/fields/R/interp.surface.R | 6 fields-18.0/fields/R/interp.surface.grid.R | 2 fields-18.0/fields/R/larry.colors.R | 2 fields-18.0/fields/R/mKrig.R | 40 fields-18.0/fields/R/mKrigCheckXY.R | 12 fields-18.0/fields/R/mKrigFastPredict.R | 12 fields-18.0/fields/R/mKrigFastPredictSetup.R | 2 fields-18.0/fields/R/mKrigMLEGrid.R | 2 fields-18.0/fields/R/mKrigMLEJoint.R | 10 fields-18.0/fields/R/mKrigMisc.R | 8 fields-18.0/fields/R/make.surface.grid.R | 2 fields-18.0/fields/R/makeMultiIndex.R | 4 fields-18.0/fields/R/matern.image.cov.R | 4 fields-18.0/fields/R/minimax.crit.R | 2 fields-18.0/fields/R/multWendlandGrid.R | 2 fields-18.0/fields/R/naturalSplineBasis.R |only fields-18.0/fields/R/offGridWeights.R | 4 fields-18.0/fields/R/offGridWeights1D.R | 10 fields-18.0/fields/R/offGridWeights2D.R | 12 fields-18.0/fields/R/panelPlotCommonAxesNew.R |only fields-18.0/fields/R/parse.grid.list.R | 2 fields-18.0/fields/R/plot.Krig.R | 2 fields-18.0/fields/R/plot.spatialDesign.R | 2 fields-18.0/fields/R/plot.spatialProcess.R | 4 fields-18.0/fields/R/plot.sreg.R | 2 fields-18.0/fields/R/plot.surface.R | 4 fields-18.0/fields/R/plot.vgram.matrix.R | 2 fields-18.0/fields/R/plotMatrix.R | 21 fields-18.0/fields/R/poly.image.R | 4 fields-18.0/fields/R/predict.Krig.R | 4 fields-18.0/fields/R/predict.fastTps.R | 4 fields-18.0/fields/R/predict.interp.surface.R | 2 fields-18.0/fields/R/predict.mKrig.R | 6 fields-18.0/fields/R/predict.sreg.R | 2 fields-18.0/fields/R/predictDerivative.Krig.R | 8 fields-18.0/fields/R/predictSE.Krig.R | 4 fields-18.0/fields/R/predictSE.R | 2 fields-18.0/fields/R/predictSE.mKrig.R | 4 fields-18.0/fields/R/predictSEUsingKrigA.R | 4 fields-18.0/fields/R/predictSurface.Krig.R | 4 fields-18.0/fields/R/predictSurface.family.R | 2 fields-18.0/fields/R/predictSurface.fastTps.R | 2 fields-18.0/fields/R/predictSurface.mKrig.R | 6 fields-18.0/fields/R/predictSurfaceSE.R | 6 fields-18.0/fields/R/print.Krig.R | 2 fields-18.0/fields/R/print.mKrig.R | 2 fields-18.0/fields/R/print.mKrig.summary.R | 2 fields-18.0/fields/R/print.spatial.design.R | 2 fields-18.0/fields/R/print.spatialProcess.R | 2 fields-18.0/fields/R/print.spatialProcessSummary.R | 2 fields-18.0/fields/R/print.sreg.R | 2 fields-18.0/fields/R/print.summary.Krig.R | 2 fields-18.0/fields/R/print.summary.sreg.R | 2 fields-18.0/fields/R/print.summarySpatialDesign.R | 2 fields-18.0/fields/R/printGCVWarnings.R | 2 fields-18.0/fields/R/profile.R | 2 fields-18.0/fields/R/profileCI.R | 2 fields-18.0/fields/R/profileMLE.R | 6 fields-18.0/fields/R/qr.q2ty.R | 2 fields-18.0/fields/R/qr.yq2.R | 2 fields-18.0/fields/R/qsreg.family.R | 6 fields-18.0/fields/R/quantilePlot.R |only fields-18.0/fields/R/quickPrint.R | 2 fields-18.0/fields/R/quilt.plot.R | 2 fields-18.0/fields/R/rad.cov.R | 4 fields-18.0/fields/R/rad.image.cov.R | 2 fields-18.0/fields/R/rad.simple.cov.R | 2 fields-18.0/fields/R/radbas.constant.R | 2 fields-18.0/fields/R/rdist.R | 2 fields-18.0/fields/R/rdist.earth.R | 2 fields-18.0/fields/R/rdist.earth.vec.R | 2 fields-18.0/fields/R/rdist.vec.R | 2 fields-18.0/fields/R/residuals.Krig.R | 2 fields-18.0/fields/R/ribbon.plot.R | 2 fields-18.0/fields/R/set.panel.R | 2 fields-18.0/fields/R/setup.image.smooth.R | 4 fields-18.0/fields/R/sim.Krig.R | 4 fields-18.0/fields/R/sim.rf.R | 2 fields-18.0/fields/R/sim.spatialProcess.R | 6 fields-18.0/fields/R/simLocal.spatialProcess.R | 4 fields-18.0/fields/R/simSpatialData.R | 6 fields-18.0/fields/R/smooth.2d.R | 2 fields-18.0/fields/R/snow.colors.R | 2 fields-18.0/fields/R/spam_2lz.R | 4 fields-18.0/fields/R/spatialProcess.R | 22 fields-18.0/fields/R/spatialProcessSetDefaults.R | 44 fields-18.0/fields/R/splint.R | 4 fields-18.0/fields/R/sreg.family.R | 2 fields-18.0/fields/R/stationary.cov.R | 10 fields-18.0/fields/R/stationary.image.cov.R | 6 fields-18.0/fields/R/stationary.taper.cov.R | 6 fields-18.0/fields/R/stationaryImageCov.R | 2 fields-18.0/fields/R/stats.R | 2 fields-18.0/fields/R/stats.bin.R | 2 fields-18.0/fields/R/summary.Krig.R | 2 fields-18.0/fields/R/summary.mKrig.R | 2 fields-18.0/fields/R/summary.ncdf.R | 2 fields-18.0/fields/R/summary.spatialDesign.R | 2 fields-18.0/fields/R/summary.spatialProcess.R | 4 fields-18.0/fields/R/summary.sreg.R | 2 fields-18.0/fields/R/summaryGCV.Krig.R | 2 fields-18.0/fields/R/summaryGCV.sreg.R | 2 fields-18.0/fields/R/supportsArg.R | 2 fields-18.0/fields/R/surface.family.R | 4 fields-18.0/fields/R/test.for.zero.R | 2 fields-18.0/fields/R/tim.colors.R | 4 fields-18.0/fields/R/transformx.R | 2 fields-18.0/fields/R/unrollZGrid.R | 2 fields-18.0/fields/R/unscale.R | 2 fields-18.0/fields/R/vgram.family.R | 2 fields-18.0/fields/R/vgram.matrix.R | 6 fields-18.0/fields/R/wendland.family.R | 32 fields-18.0/fields/R/wendland.image.cov.R | 6 fields-18.0/fields/R/which.max.matrix.R | 2 fields-18.0/fields/R/world.R | 2 fields-18.0/fields/R/xline.R | 2 fields-18.0/fields/R/yline.R | 2 fields-18.0/fields/data/AudiA4.rda |only fields-18.0/fields/data/BD.rda |only fields-18.0/fields/data/ChicagoO3.rda |only fields-18.0/fields/data/RMprecip.rda |only fields-18.0/fields/data/datalist | 18 fields-18.0/fields/data/flame.rda |only fields-18.0/fields/data/minitri.rda |only fields-18.0/fields/man/AudiA4.Rd |only fields-18.0/fields/man/BD.Rd | 53 - fields-18.0/fields/man/CO.Rd | 169 --- fields-18.0/fields/man/CO2.Rd | 40 fields-18.0/fields/man/CovarianceUpper.Rd | 20 fields-18.0/fields/man/Exponential.Rd | 66 - fields-18.0/fields/man/FORTRAN.internal.Rd | 20 fields-18.0/fields/man/Krig.Amatrix.Rd | 86 - fields-18.0/fields/man/Krig.Rd | 464 ++++----- fields-18.0/fields/man/Krig.engine.default.Rd | 144 +- fields-18.0/fields/man/Krig.null.function.Rd | 18 fields-18.0/fields/man/Krig.replicates.Rd | 38 fields-18.0/fields/man/KrigFindLambda.Rd | 81 - fields-18.0/fields/man/LENSExample.Rd | 56 - fields-18.0/fields/man/NorthAmericanRainfall.Rd | 44 fields-18.0/fields/man/QTps.Rd | 144 +- fields-18.0/fields/man/RCMexample.Rd | 34 fields-18.0/fields/man/RMprecip.Rd | 54 - fields-18.0/fields/man/Tps.Rd | 123 +- fields-18.0/fields/man/US.Rd | 8 fields-18.0/fields/man/US.dat.Rd | 8 fields-18.0/fields/man/Wendland.Rd | 34 fields-18.0/fields/man/WorldBank.Rd | 34 fields-18.0/fields/man/add.image.Rd | 10 fields-18.0/fields/man/arrow.plot.Rd | 34 fields-18.0/fields/man/as.image.Rd | 37 fields-18.0/fields/man/as.surface.Rd | 30 fields-18.0/fields/man/bplot.Rd | 34 fields-18.0/fields/man/bplot.xy.Rd | 18 fields-18.0/fields/man/colorbar.plot.Rd | 38 fields-18.0/fields/man/compactToMat.Rd | 6 fields-18.0/fields/man/cover.design.Rd | 75 - fields-18.0/fields/man/drape.plot.Rd | 60 - fields-18.0/fields/man/envelopePlot.Rd | 8 fields-18.0/fields/man/exp.cov.Rd | 197 ++- fields-18.0/fields/man/fields-internal.Rd | 7 fields-18.0/fields/man/fields-stuff.Rd | 48 fields-18.0/fields/man/fields.Rd | 130 +- fields-18.0/fields/man/fields.grid.Rd | 13 fields-18.0/fields/man/fields.hints.Rd | 8 fields-18.0/fields/man/fields.tests.Rd | 30 fields-18.0/fields/man/flame.Rd | 26 fields-18.0/fields/man/glacier.Rd | 28 fields-18.0/fields/man/grid.list.Rd | 82 - fields-18.0/fields/man/image.cov.Rd | 70 - fields-18.0/fields/man/image.plot.Rd | 347 ++---- fields-18.0/fields/man/image.smooth.Rd | 29 fields-18.0/fields/man/image2lz.Rd | 50 fields-18.0/fields/man/imagePlot.Rd | 482 ++++----- fields-18.0/fields/man/interp.surface.Rd | 44 fields-18.0/fields/man/lennon.Rd | 4 fields-18.0/fields/man/mKrig.Rd | 176 +-- fields-18.0/fields/man/mKrigMLE.Rd | 104 +- fields-18.0/fields/man/minitri.Rd | 29 fields-18.0/fields/man/naturalSplineBasis.Rd |only fields-18.0/fields/man/offGridWeights.Rd | 104 +- fields-18.0/fields/man/ozone.Rd | 21 fields-18.0/fields/man/ozone2.Rd | 32 fields-18.0/fields/man/panelPlot.Rd | 572 +++++++++-- fields-18.0/fields/man/plot.Krig.Rd | 25 fields-18.0/fields/man/plot.surface.Rd | 33 fields-18.0/fields/man/poly.image.Rd | 42 fields-18.0/fields/man/predict.Krig.Rd | 53 - fields-18.0/fields/man/predictSE.Krig.Rd | 48 fields-18.0/fields/man/predictSurface.Rd | 108 +- fields-18.0/fields/man/print.Krig.Rd | 7 fields-18.0/fields/man/pushpin.Rd | 12 fields-18.0/fields/man/qsreg.Rd | 55 - fields-18.0/fields/man/quantilePlot.Rd |only fields-18.0/fields/man/quilt.plot.Rd | 167 +-- fields-18.0/fields/man/rat.diet.Rd | 25 fields-18.0/fields/man/rdist.Rd | 38 fields-18.0/fields/man/rdist.earth.Rd | 32 fields-18.0/fields/man/registeredC.Rd | 28 fields-18.0/fields/man/ribbon.plot.Rd | 10 fields-18.0/fields/man/set.panel.Rd | 16 fields-18.0/fields/man/sim.Krig.Rd | 179 ++- fields-18.0/fields/man/sim.rf.Rd | 82 - fields-18.0/fields/man/smooth.2d.Rd | 76 - fields-18.0/fields/man/spam2lz.Rd | 29 fields-18.0/fields/man/spatialProcess.Rd | 212 ++-- fields-18.0/fields/man/splint.Rd | 35 fields-18.0/fields/man/sreg.Rd | 88 - fields-18.0/fields/man/stats.Rd | 8 fields-18.0/fields/man/stats.bin.Rd | 14 fields-18.0/fields/man/summary.Krig.Rd | 9 fields-18.0/fields/man/summary.ncdf.Rd | 14 fields-18.0/fields/man/supportsArg.Rd | 10 fields-18.0/fields/man/surface.Krig.Rd | 26 fields-18.0/fields/man/tim.colors.Rd | 71 - fields-18.0/fields/man/transformx.Rd | 19 fields-18.0/fields/man/vgram.Rd | 38 fields-18.0/fields/man/vgram.matrix.Rd | 26 fields-18.0/fields/man/world.Rd | 8 fields-18.0/fields/man/xline.Rd | 8 fields-18.0/fields/man/yline.Rd | 11 fields-18.0/fields/tests/Krig.Z.test.R | 24 fields-18.0/fields/tests/Krig.Z.test.Rout.save | 8 fields-18.0/fields/tests/Krig.se.W.R | 8 fields-18.0/fields/tests/Krig.se.W.Rout.save | 8 fields-18.0/fields/tests/Krig.se.grid.test.R | 14 fields-18.0/fields/tests/Krig.se.grid.test.Rout.save | 8 fields-18.0/fields/tests/Krig.se.test.R | 32 fields-18.0/fields/tests/Krig.se.test.Rout.save | 40 fields-18.0/fields/tests/Krig.test.R | 17 fields-18.0/fields/tests/Krig.test.Rout.save | 8 fields-18.0/fields/tests/Krig.test.W.R | 14 fields-18.0/fields/tests/Krig.test.W.Rout.save | 8 fields-18.0/fields/tests/KrigGCVREML.test.R | 6 fields-18.0/fields/tests/KrigGCVREML.test.Rout.save | 8 fields-18.0/fields/tests/Likelihood.test.R | 2 fields-18.0/fields/tests/Likelihood.test.Rout.save | 8 fields-18.0/fields/tests/SEFixedParameters.R | 3 fields-18.0/fields/tests/SEFixedParameters.Rout.save | 8 fields-18.0/fields/tests/Tps.test.R | 4 fields-18.0/fields/tests/Tps.test.Rout.save | 8 fields-18.0/fields/tests/Wend.test.R | 20 fields-18.0/fields/tests/Wend.test.Rout.save | 8 fields-18.0/fields/tests/cov.test.R | 12 fields-18.0/fields/tests/cov.test.Rout.save | 8 fields-18.0/fields/tests/cov.test2.R | 12 fields-18.0/fields/tests/cov.test2.Rout.save | 8 fields-18.0/fields/tests/derivative.test.R | 54 - fields-18.0/fields/tests/derivative.test.Rout.save | 8 fields-18.0/fields/tests/diag.multiply.test.Rout.save | 8 fields-18.0/fields/tests/evlpoly.test.R | 10 fields-18.0/fields/tests/evlpoly.test.Rout.save | 8 fields-18.0/fields/tests/fastTpsPredict.test.Rout.save | 8 fields-18.0/fields/tests/mKrig.Z.Rout.save | 8 fields-18.0/fields/tests/mKrig.parameters.test.R | 8 fields-18.0/fields/tests/mKrig.parameters.test.Rout.save | 16 fields-18.0/fields/tests/mKrig.se.test.R | 14 fields-18.0/fields/tests/mKrig.se.test.Rout.save | 8 fields-18.0/fields/tests/mKrig.test.R | 76 - fields-18.0/fields/tests/mKrig.test.Rout.save | 8 fields-18.0/fields/tests/mKrigMLETest.Rout.save | 8 fields-18.0/fields/tests/mKrigREMLTest.Rout.save | 8 fields-18.0/fields/tests/misc.test.Rout.save | 8 fields-18.0/fields/tests/offGridWeights.test.Rout.save | 8 fields-18.0/fields/tests/offGridWeightsNEW.test.Rout.save | 8 fields-18.0/fields/tests/spam.test.R | 34 fields-18.0/fields/tests/spam.test.Rout.save | 8 fields-18.0/fields/tests/sreg.test.R | 23 fields-18.0/fields/tests/sreg.test.Rout.save | 8 fields-18.0/fields/tests/testO3LocalExample.Rout.save | 8 fields-18.0/fields/tests/testZCommon.Rout.save | 8 fields-18.0/fields/tests/vgram.test.R | 16 fields-18.0/fields/tests/vgram.test.Rout.save | 8 fields-18.0/fields/tests/vgram2.test.R | 16 fields-18.0/fields/tests/vgram2.test.Rout.save | 8 369 files changed, 4842 insertions(+), 4168 deletions(-)
Title: Tidy Epidemiological Rates
Description: Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, using internal statistical calculations.
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Diff between tidyrates versions 0.0.1 dated 2024-03-19 and 0.0.2 dated 2026-10-13
DESCRIPTION | 16 ++++++++------- MD5 | 29 +++++++++++++++------------- NEWS.md | 33 ++++++++++++++++++++++++++++++++ R/adjustment.R |only R/rate_adj_direct.R | 4 +-- R/rate_adj_indirect.R | 12 +++++------ README.md | 17 ++++++++++------ build/vignette.rds |binary inst/doc/quickstart.R | 2 - inst/doc/quickstart.Rmd | 6 ++--- inst/doc/quickstart.html | 23 ++++++++++++---------- man/rate_adj_direct.Rd | 2 - man/rate_adj_indirect.Rd | 6 ++--- tests/testthat/helper-legacy-rates.R |only tests/testthat/test-adjustment.R |only tests/testthat/test-rate_adj_indirect.R | 12 +++++++++++ vignettes/quickstart.Rmd | 6 ++--- 17 files changed, 113 insertions(+), 55 deletions(-)
Title: Access your Coletum's Data from API
Description: Get your data (forms, structures, answers) from Coletum
<https://coletum.com> to handle and analyse.
Author: Andre Smaniotto [aut, cre],
Marcelo Magnani [aut],
Rodrigo Sant'Ana [aut],
GeoSapiens [cph, fnd]
Maintainer: Andre Smaniotto <smaniotto@geosapiens.com.br>
Diff between RColetum versions 1.1.0 dated 2026-08-21 and 1.2.0 dated 2026-10-13
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NEWS.md | 11 +++++++++++ R/GetForm.R | 5 ++++- R/utils.R | 13 ++++++++++++- man/GetForm.Rd | 5 ++++- tests/testthat/test-SeparatorComponents.R |only tests/testthat/test-UserAgent.R |only 8 files changed, 42 insertions(+), 12 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] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 7.1.0 dated 2026-09-20 and 7.2.0 dated 2026-10-13
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nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nls.R | 245 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-nonmem-pktime-1167.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npInner.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-error-models.R | 8 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-fixed.R | 18 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-npag-general-lik.R | 93 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-ofv.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-omega-block.R | 41 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-optim.R | 35 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-progress-bar-1171.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-resid-ode-fallback.R | 56 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-resid.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-rxuideparse.R | 271 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-cov-analytic.R | 67 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-cov-sa.R | 241 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-degraded-fit.R | 81 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-iov-twolevel-fit.R | 32 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-mix-ofv.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-mix.R | 74 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem-nearpd.R | 2 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-saem.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-scale-normtype.R | 162 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21-hessian.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21-ratio.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shi21.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-shierr-positive.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-simModelLag.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-sqrtm.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-tolFactor.R | 52 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-trust.R | 91 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vae-errmodel.R | 3 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vae-residopt.R | 41 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vi-control.R | 14 nlmixr2est-7.2.0/nlmixr2est/tests/testthat/test-vi.R |only nlmixr2est-7.2.0/nlmixr2est/tests/testthat/testthat-problems.rds |binary nlmixr2est-7.2.0/nlmixr2est/vignettes/events.Rmd |only 285 files changed, 17285 insertions(+), 12758 deletions(-)
Title: Builds the 'TinyCC' Command-Line Interface and Library for 'C'
Scripting in 'R'
Description: Builds the 'TinyCC' (Tiny 'C' Compiler) command-line interface
and library for package use in 'R'. The package compiles 'TinyCC' from source and
provides R functions to interact with the compiler. 'TinyCC' can be
used for header preprocessing, just-in-time compilation of 'C' code in
'R', and lightweight 'C' scripting workflows.
Author: Sounkou Mahamane Toure [aut, cre],
Mike Cheng [cph] ,
Adam Dunkels [ctb] ,
Swedish Institute of Computer Science [cph] ,
Fabrice Bellard and TinyCC authors [cph] ,
Brian Lee Yung Rowe [ctb, cph]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rtinycc versions 0.1.15 dated 2026-07-25 and 0.1.16 dated 2026-10-13
Rtinycc-0.1.15/Rtinycc/src/tinycc-199f07b.tar.gz |only Rtinycc-0.1.16/Rtinycc/DESCRIPTION | 20 +++-- Rtinycc-0.1.16/Rtinycc/MD5 | 32 +++++---- Rtinycc-0.1.16/Rtinycc/NAMESPACE | 2 Rtinycc-0.1.16/Rtinycc/NEWS.md | 6 + Rtinycc-0.1.16/Rtinycc/R/aaa.R | 1 Rtinycc-0.1.16/Rtinycc/R/aaa_ffi_codegen_dispatch.R |only Rtinycc-0.1.16/Rtinycc/R/aaa_ffi_codegen_rules.R | 8 +- Rtinycc-0.1.16/Rtinycc/configure.win | 16 ++++ Rtinycc-0.1.16/Rtinycc/inst/LICENSE.note | 23 +++++- Rtinycc-0.1.16/Rtinycc/inst/doc/compilation-and-call-overhead.html | 20 ++--- Rtinycc-0.1.16/Rtinycc/inst/doc/ffi-helpers.html | 8 +- Rtinycc-0.1.16/Rtinycc/inst/doc/getting-started.html | 12 +-- Rtinycc-0.1.16/Rtinycc/inst/doc/internals.Rmd | 27 +++---- Rtinycc-0.1.16/Rtinycc/inst/doc/internals.html | 34 ++++------ Rtinycc-0.1.16/Rtinycc/inst/tinytest/test_codegen_dispatch.R |only Rtinycc-0.1.16/Rtinycc/src/tinycc-1bed0f3.tar.gz |only Rtinycc-0.1.16/Rtinycc/tools/vendortinycc.R | 6 - Rtinycc-0.1.16/Rtinycc/vignettes/internals.Rmd | 27 +++---- 19 files changed, 133 insertions(+), 109 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel [aut, cre] ,
Khanh Nguyen [aut] ,
Terry Leitch [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.28 dated 2026-07-10 and 0.4.29 dated 2026-10-13
ChangeLog | 92 ++++++++++++++++++++++++ DESCRIPTION | 8 +- MD5 | 72 +++++++++---------- R/affine.R | 8 +- R/arrays.R | 2 R/bermudan.R | 2 R/bond.R | 148 ++++++++++++++++++++------------------- R/calendars.R | 19 ++++- R/datasets.R | 2 R/discount.R | 2 R/implied.R | 1 README.md | 6 - configure | 25 +++--- configure.ac | 18 +++- inst/NEWS.Rd | 27 ++++++- man/AffineSwaption.Rd | 8 +- man/AsianOption.Rd | 2 man/BermudanSwaption.Rd | 4 - man/Bond.Rd | 2 man/CallableBond.Rd | 6 - man/ConvertibleBond.Rd | 8 +- man/DiscountCurve.Rd | 4 - man/FittedBondCurve.Rd | 2 man/FixedRateBond.Rd | 4 - man/FloatingRateBond.Rd | 8 +- man/ImpliedVolatility.Rd | 2 man/Option.Rd | 2 man/SabrSwaption.Rd | 20 ++--- man/Schedule.Rd | 2 man/ZeroCouponBond.Rd | 57 +++++++-------- man/tsQuotes.Rd | 2 src/Makevars.in | 5 - src/Makevars.win | 11 +- src/calendars.cpp | 174 +++++++++++++++++++++++++++++++++++------------ src/sabr.cpp | 20 +++++ src/utils.cpp | 10 +- tests/tinytest.R | 12 --- 37 files changed, 521 insertions(+), 276 deletions(-)
Title: Missing Cost Effectiveness Models
Description: Performs Bayesian cost-effectiveness analysis with missing outcome data. Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models. The package allows to assess model convergence and summarise the statistical and economic results using different types of measures and graphs. The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Author: Andrea Gabrio [aut, cre, cph]
Maintainer: Andrea Gabrio <a.gabrio@maastrichtuniversity.nl>
Diff between missingHE versions 1.6.1 dated 2026-06-01 and 1.6.2 dated 2026-10-13
missingHE-1.6.1/missingHE/README.md |only missingHE-1.6.2/missingHE/DESCRIPTION | 27 - missingHE-1.6.2/missingHE/MD5 | 173 +++--- missingHE-1.6.2/missingHE/NAMESPACE | 108 ++-- missingHE-1.6.2/missingHE/R/anyBars.R | 2 missingHE-1.6.2/missingHE/R/coef.missingHE.R | 39 - missingHE-1.6.2/missingHE/R/data_read_hurdle.R | 2 missingHE-1.6.2/missingHE/R/data_read_lmdm.R | 2 missingHE-1.6.2/missingHE/R/data_read_pattern.R | 2 missingHE-1.6.2/missingHE/R/data_read_selection.R | 2 missingHE-1.6.2/missingHE/R/diagnostic.R | 2 missingHE-1.6.2/missingHE/R/fb.R | 2 missingHE-1.6.2/missingHE/R/hurdle.R | 54 +- missingHE-1.6.2/missingHE/R/isAnyArgBar.R | 2 missingHE-1.6.2/missingHE/R/isBar.R | 2 missingHE-1.6.2/missingHE/R/jagsresults.R | 4 missingHE-1.6.2/missingHE/R/lmdm.R | 61 ++ missingHE-1.6.2/missingHE/R/nobars_.R | 2 missingHE-1.6.2/missingHE/R/pattern.R | 35 + missingHE-1.6.2/missingHE/R/postsum.R |only missingHE-1.6.2/missingHE/R/ppc.R | 87 ++- missingHE-1.6.2/missingHE/R/print.missingHE.R | 117 +--- missingHE-1.6.2/missingHE/R/prior_hurdle.R | 2 missingHE-1.6.2/missingHE/R/prior_lmdm.R | 2 missingHE-1.6.2/missingHE/R/prior_pattern.R | 2 missingHE-1.6.2/missingHE/R/prior_selection.R | 2 missingHE-1.6.2/missingHE/R/run_hurdle.R | 12 missingHE-1.6.2/missingHE/R/run_lmdm.R | 18 missingHE-1.6.2/missingHE/R/run_pattern.R | 14 missingHE-1.6.2/missingHE/R/run_selection.R | 12 missingHE-1.6.2/missingHE/R/selection.R | 30 + missingHE-1.6.2/missingHE/R/summary.missingHE.R | 2 missingHE-1.6.2/missingHE/R/write_hurdle.R | 2 missingHE-1.6.2/missingHE/R/write_lmdm.R | 2 missingHE-1.6.2/missingHE/R/write_pattern.R | 2 missingHE-1.6.2/missingHE/R/write_selection.R | 2 missingHE-1.6.2/missingHE/build/vignette.rds |binary missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.R | 140 ++--- missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.Rmd | 212 ++++---- missingHE-1.6.2/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.html | 162 +++--- missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.R | 33 - missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.Rmd | 199 ++++--- missingHE-1.6.2/missingHE/inst/doc/Introduction_to_missingHE.html | 169 +++--- missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.R | 16 missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.Rmd | 118 ++-- missingHE-1.6.2/missingHE/inst/doc/Longitudinal_models_in_missingHE.html | 250 ++++------ missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.R | 68 +- missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.Rmd | 160 +++--- missingHE-1.6.2/missingHE/inst/doc/Model_customisation_in_missingHE.html | 226 ++++----- missingHE-1.6.2/missingHE/man/MenSS.Rd | 61 +- missingHE-1.6.2/missingHE/man/PBS.Rd | 92 +-- missingHE-1.6.2/missingHE/man/anyBars.Rd | 4 missingHE-1.6.2/missingHE/man/coef.missingHE.Rd | 2 missingHE-1.6.2/missingHE/man/data_read_hurdle.Rd | 23 missingHE-1.6.2/missingHE/man/data_read_lmdm.Rd | 15 missingHE-1.6.2/missingHE/man/data_read_pattern.Rd | 7 missingHE-1.6.2/missingHE/man/data_read_selection.Rd | 15 missingHE-1.6.2/missingHE/man/diagnostic.Rd | 14 missingHE-1.6.2/missingHE/man/fb.Rd | 4 missingHE-1.6.2/missingHE/man/hurdle.Rd | 72 +- missingHE-1.6.2/missingHE/man/isAnyArgBar.Rd | 4 missingHE-1.6.2/missingHE/man/isBar.Rd | 4 missingHE-1.6.2/missingHE/man/jagsresults.Rd | 26 - missingHE-1.6.2/missingHE/man/lmdm.Rd | 52 +- missingHE-1.6.2/missingHE/man/nobars_.Rd | 4 missingHE-1.6.2/missingHE/man/pattern.Rd | 58 +- missingHE-1.6.2/missingHE/man/pic.Rd | 62 +- missingHE-1.6.2/missingHE/man/plot.missingHE.Rd | 8 missingHE-1.6.2/missingHE/man/postsum.Rd |only missingHE-1.6.2/missingHE/man/ppc.Rd | 12 missingHE-1.6.2/missingHE/man/print.missingHE.Rd | 36 - missingHE-1.6.2/missingHE/man/prior_hurdle.Rd | 9 missingHE-1.6.2/missingHE/man/prior_lmdm.Rd | 11 missingHE-1.6.2/missingHE/man/prior_pattern.Rd | 10 missingHE-1.6.2/missingHE/man/prior_selection.Rd | 9 missingHE-1.6.2/missingHE/man/run_hurdle.Rd | 5 missingHE-1.6.2/missingHE/man/run_lmdm.Rd | 7 missingHE-1.6.2/missingHE/man/run_pattern.Rd | 6 missingHE-1.6.2/missingHE/man/run_selection.Rd | 5 missingHE-1.6.2/missingHE/man/selection.Rd | 50 +- missingHE-1.6.2/missingHE/man/summary.missingHE.Rd | 2 missingHE-1.6.2/missingHE/man/write_hurdle.Rd | 8 missingHE-1.6.2/missingHE/man/write_lmdm.Rd | 10 missingHE-1.6.2/missingHE/man/write_pattern.Rd | 9 missingHE-1.6.2/missingHE/man/write_selection.Rd | 8 missingHE-1.6.2/missingHE/vignettes/Fitting_MNAR_models_in_missingHE.Rmd | 212 ++++---- missingHE-1.6.2/missingHE/vignettes/Introduction_to_missingHE.Rmd | 199 ++++--- missingHE-1.6.2/missingHE/vignettes/Longitudinal_models_in_missingHE.Rmd | 118 ++-- missingHE-1.6.2/missingHE/vignettes/Model_customisation_in_missingHE.Rmd | 160 +++--- 89 files changed, 1990 insertions(+), 2005 deletions(-)
Title: Create Common Tables and Listings Used in Clinical Trials
Description: Structure and formatting requirements for clinical trial table and listing outputs
vary between pharmaceutical companies. 'junco' provides additional tooling for use alongside
the 'rtables', 'rlistings' and 'tern' packages when creating table and listing outputs. While
motivated by the specifics of Johnson and Johnson Clinical and Statistical Programming's
table and listing shells, 'junco' provides functionality that is general and reusable.
Major features include a) alternative and extended statistical analyses beyond what 'tern'
supports for use in standard safety and efficacy tables, b) a robust production-grade
Rich Text Format (RTF) and DOCX exporter for tables, listings and graphs, c) structural support
for spanning column headers and risk difference columns in tables, and d) robust
font-aware automatic column width algorithms for both listings and tables.
Author: Gabriel Becker [cre, aut] ,
Ilse Augustyns [aut],
Paul Jenkins [aut],
Daniel Hofstaedter [aut],
Joseph Kovach [aut],
David Munoz Tord [aut],
Daniel Sabanes Bove [aut],
Ezequiel Anokian [ctb],
Renfei Mao [ctb],
Mrinal Das [ctb],
Wojciech Wojciak [ctb] [...truncated...]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between junco versions 0.1.6 dated 2026-05-10 and 0.1.7 dated 2026-10-13
junco-0.1.6/junco/R/a_summary.r |only junco-0.1.6/junco/R/a_summary_diff_mvars.r |only junco-0.1.6/junco/R/count_denom_fraction.R |only junco-0.1.6/junco/R/coxph_hr.R |only junco-0.1.6/junco/R/filter_df_prior_afun.r |only junco-0.1.6/junco/R/kaplan_meier.R |only junco-0.1.6/junco/R/rbmi.R |only junco-0.1.6/junco/R/s_diff_mean_ci.r |only junco-0.1.6/junco/R/s_summary_diff.r |only junco-0.1.6/junco/R/safe_t_test.r |only junco-0.1.6/junco/man/a_summary_diff_mvars.Rd |only junco-0.1.6/junco/man/c_summary_subset_label.Rd |only junco-0.1.6/junco/man/coxph_hr.Rd |only junco-0.1.6/junco/man/filter_df_prior_afun.Rd |only junco-0.1.6/junco/man/h_get_trtvar_refpath.Rd |only junco-0.1.6/junco/man/kaplan_meier.Rd |only junco-0.1.6/junco/man/postfun_eq5d.Rd |only junco-0.1.6/junco/man/s_diff_mean_ci.Rd |only junco-0.1.6/junco/man/safe_t_test.Rd |only junco-0.1.6/junco/tests/testthat/_snaps/coxph_hr.md |only junco-0.1.6/junco/tests/testthat/_snaps/kaplan_meier.md |only 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junco-0.1.7/junco/R/a_two_tier.R | 206 +++ junco-0.1.7/junco/R/ancova.R | 11 junco-0.1.7/junco/R/blank_line.R | 114 + junco-0.1.7/junco/R/column_stats.R | 290 +++- junco-0.1.7/junco/R/colwidths.R | 62 - junco-0.1.7/junco/R/cond_proportion_diff.R |only junco-0.1.7/junco/R/cond_proportion_j.R |only junco-0.1.7/junco/R/coxreg_multivar.R | 21 junco-0.1.7/junco/R/cur_col_split_path_utils.R |only junco-0.1.7/junco/R/deprecate.R |only junco-0.1.7/junco/R/docx_exporter_functions.R | 79 - junco-0.1.7/junco/R/estimate_proportion_diff.R | 94 - junco-0.1.7/junco/R/event_free.R | 15 junco-0.1.7/junco/R/get_ref_info.R | 125 +- junco-0.1.7/junco/R/h_eair_funs.R | 76 + junco-0.1.7/junco/R/h_freq_funs.R | 151 +- junco-0.1.7/junco/R/jjcsformats.R | 253 ++++ junco-0.1.7/junco/R/jjcsformats_d.R |only junco-0.1.7/junco/R/junco-package.R | 2 junco-0.1.7/junco/R/junco_utils_default_stats_formats_labels.R | 176 ++ junco-0.1.7/junco/R/odds_ratio.R | 41 junco-0.1.7/junco/R/pool_funs.R |only 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Title: Assurance Methods for Clinical Trials with a Delayed Treatment
Effect
Description: Provides functions for planning clinical trials subject to a delayed
treatment effect using assurance-based methods. Includes two 'shiny'
applications for interactive exploration, simulation, and visualisation of
trial designs and outcomes. The methodology is described in:
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Assurance methods for designing a clinical trial with a delayed treatment
effect" <doi:10.1002/sim.10136>,
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Adaptive clinical trial design with delayed treatment effects using
elicited prior distributions" <doi:10.48550/arXiv.2509.07602>.
Author: James Salsbury [aut, cre]
Maintainer: James Salsbury <jsalsbury1@sheffield.ac.uk>
Diff between DTEAssurance versions 1.1.0 dated 2025-12-02 and 1.3.0 dated 2026-10-13
DTEAssurance-1.1.0/DTEAssurance/man/BPP_func.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_threshold.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_timing.Rd |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-BPP_func.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_threshold.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_timing.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-make_rpact_design_from_GSD_model.R |only DTEAssurance-1.3.0/DTEAssurance/DESCRIPTION | 16 DTEAssurance-1.3.0/DTEAssurance/LICENSE | 4 DTEAssurance-1.3.0/DTEAssurance/MD5 | 96 DTEAssurance-1.3.0/DTEAssurance/NAMESPACE | 52 DTEAssurance-1.3.0/DTEAssurance/NEWS.md | 198 DTEAssurance-1.3.0/DTEAssurance/R/deprecated.R |only DTEAssurance-1.3.0/DTEAssurance/R/helpers.R |only DTEAssurance-1.3.0/DTEAssurance/R/main.R | 1446 ++-- DTEAssurance-1.3.0/DTEAssurance/R/paired.R |only DTEAssurance-1.3.0/DTEAssurance/R/shiny_apps.R | 42 DTEAssurance-1.3.0/DTEAssurance/R/utils.R | 1090 ++- DTEAssurance-1.3.0/DTEAssurance/README.md | 471 - DTEAssurance-1.3.0/DTEAssurance/inst/shiny/adaptive_app/app.R | 362 - DTEAssurance-1.3.0/DTEAssurance/inst/shiny/adaptive_app/rsconnect |only DTEAssurance-1.3.0/DTEAssurance/inst/shiny/assurance_app/app.R | 3301 ++++------ DTEAssurance-1.3.0/DTEAssurance/inst/shiny/assurance_app/rsconnect |only DTEAssurance-1.3.0/DTEAssurance/man/DTEAssurance-deprecated.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/PP_func.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/apply_GSD_to_trial.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/apply_design_rule.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/assurance_adaptive_shiny_app.Rd | 46 DTEAssurance-1.3.0/DTEAssurance/man/calc_dte_assurance.Rd | 202 DTEAssurance-1.3.0/DTEAssurance/man/calc_dte_assurance_adaptive.Rd | 253 DTEAssurance-1.3.0/DTEAssurance/man/calibrate_PP_threshold.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/calibrate_PP_timing.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/calibrate_matched_futility_boundary.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/cens_data.Rd | 106 DTEAssurance-1.3.0/DTEAssurance/man/compute_relative_floors.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/figures/README-unnamed-chunk-8-1.png |binary DTEAssurance-1.3.0/DTEAssurance/man/figures/README-unnamed-chunk-9-1.png |binary DTEAssurance-1.3.0/DTEAssurance/man/make_gsd_design.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/run_calibration_grid.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/run_paired_scenario.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/select_kappa_star.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/sim_dte.Rd | 94 DTEAssurance-1.3.0/DTEAssurance/man/single_matched_futility_rep.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/single_paired_rep.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/summarize_grid_by_kappa.Rd |only DTEAssurance-1.3.0/DTEAssurance/man/survival_test.Rd | 129 DTEAssurance-1.3.0/DTEAssurance/man/update_priors.Rd | 227 DTEAssurance-1.3.0/DTEAssurance/tests/testthat.R | 4 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/fixtures |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/helper-paired.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func_equivalence.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-PP_func_exp_weibull.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-apply_GSD_to_trial.R | 117 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-assurance_shiny_app.R | 26 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calc_dte_assurance_adaptive.R | 18 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calibrate_PP_threshold.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-calibrate_PP_timing.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-deprecated.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-design_rules.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-event_cuts.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-futility_types.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-kappa_selection.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-make_gsd_design.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-paired.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-refactor_equivalence.R |only DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-simulate_trial_with_recruitment.R | 8 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-single_calibration_rep.R | 8 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-survival_test.R | 77 DTEAssurance-1.3.0/DTEAssurance/tests/testthat/test-update_priors_seed.R |only 70 files changed, 4925 insertions(+), 3468 deletions(-)
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplementary tools for evaluating and validating partial least
squares structural equation models estimated with 'seminr'. Provides methods
for predictive model assessment, importance-performance analysis with
necessary condition testing, overfitting diagnostics, measurement model
verification, mediator contribution analysis, unobserved heterogeneity
detection via latent class and prediction-oriented segmentation, and
congruence coefficient testing. All functions accept estimated 'seminr'
model objects and return results with print, summary, and plot methods.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre]
Maintainer: Nicholas Patrick Danks <seminrgroup@gmail.com>
Diff between seminrExtras versions 1.0.3 dated 2026-08-19 and 1.0.4 dated 2026-10-13
DESCRIPTION | 9 MD5 | 57 ++-- NAMESPACE | 4 NEWS.md | 123 ++++++++ R/feature_congruence.R | 356 +++++++++++++++++++++----- R/feature_cta.R | 2 R/feature_cvpat.R | 83 ++---- R/helpers.R | 52 +++ README.md | 37 +- demo/00Index | 2 demo/seminr-help-debugging.R | 34 +- demo/seminr-pls-congruence.R | 36 +- demo/seminr-primer-v2-chap2.R | 4 demo/seminr-primer-v2-chap3.R | 10 demo/seminr-primer-v2-chap4.R | 5 demo/seminr-primer-v2-chap8.R | 8 inst/doc/SEMinRExtras.R | 6 inst/doc/SEMinRExtras.Rmd | 18 - inst/doc/SEMinRExtras.html | 62 ++-- man/assess_cta.Rd | 2 man/assess_cvpat.Rd | 5 man/assess_cvpat_compare.Rd | 5 man/congruence.Rd |only tests/testthat/helper-textbook.R |only tests/testthat/test-congruence-coefficients.R |only tests/testthat/test-congruence.R | 51 +++ tests/testthat/test-cvpat-reps.R |only tests/testthat/test-textbook-defaults.R |only tests/testthat/test-textbook-golden.R |only tests/testthat/test-textbook-seed-audit.R |only tests/testthat/textbook |only vignettes/SEMinRExtras.Rmd | 18 - 32 files changed, 737 insertions(+), 252 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.5.4 dated 2026-09-05 and 1.6.0 dated 2026-10-13
DESCRIPTION | 50 - MD5 | 148 ++--- NAMESPACE | 10 NEWS.md | 354 ++++++++++++ R/clean_parameters.R | 146 ++++- R/compute_variances.R | 93 ++- R/export_table.R | 416 +++++++++++++- R/find_auxiliary.R | 76 ++ R/find_formula.R | 40 + R/find_parameters.R | 52 - R/find_parameters_bayesian.R | 4 R/find_parameters_brms.R | 21 R/find_parameters_mixed.R | 7 R/find_predictors.R | 50 + R/find_random_slopes.R | 43 + R/format_table.R | 9 R/get_data.R | 242 +++++++- R/get_mixed_info.R | 51 + R/get_modelmatrix.R | 84 ++ R/get_nested_lme_varcorr.R | 46 + R/get_parameters.R | 89 ++- R/get_parameters_bayesian.R | 8 R/get_parameters_mixed.R | 7 R/get_predicted.R | 84 ++ R/get_predicted_args.R | 10 R/get_predicted_ci.R | 6 R/get_predicted_ci_zeroinflated.R | 7 R/get_predicted_mixed.R | 235 +++++++- R/get_predicted_zeroinfl.R | 19 R/get_residuals.R | 48 + R/get_sigma.R | 44 + R/get_statistic.R | 19 R/get_varcov.R | 60 +- R/get_variances.R | 14 R/is_converged.R | 655 ++++++++++++++++++++++- R/n_obs.R | 62 ++ R/null_model.R | 46 + R/utils_get_data.R | 20 R/utils_glmmtmb_ordinal.R |only inst/WORDLIST | 7 inst/doc/display.html | 370 ++++++------- man/export_table.Rd | 23 man/find_auxiliary.Rd | 4 man/find_parameters.BGGM.Rd | 4 man/get_data.Rd | 7 man/get_parameters.BGGM.Rd | 2 man/get_parameters.Rd | 1 man/get_parameters.blavaan.Rd |only man/get_predicted.Rd | 5 man/get_predicted_ci.Rd | 5 man/get_response.Rd | 7 man/get_varcov.Rd | 5 man/insight-package.Rd | 1 man/is_converged.Rd | 131 ++++ man/n_obs.Rd | 4 tests/testthat/test-blavaan.R |only tests/testthat/test-brms.R | 14 tests/testthat/test-brms_autocor.R |only tests/testthat/test-brms_dpars.R |only tests/testthat/test-brms_nonlinear.R |only tests/testthat/test-coxph.R | 15 tests/testthat/test-export_table.R | 791 +++++++++++++++++++++++++++- tests/testthat/test-find_random_slopes.R |only tests/testthat/test-format_table.R | 44 + tests/testthat/test-gamlss.R | 71 ++ tests/testthat/test-get_data-changed_data.R |only tests/testthat/test-get_modelmatrix.R | 384 +++++++++++++ tests/testthat/test-get_predicted-coxph.R |only tests/testthat/test-get_predicted-newdata.R |only tests/testthat/test-get_predicted.R | 3 tests/testthat/test-get_varcov.R | 54 + tests/testthat/test-get_variance.R | 119 ++++ tests/testthat/test-glmmTMB-ordinal.R |only tests/testthat/test-is_converged_cmdstanr.R |only tests/testthat/test-is_converged_coxph.R |only tests/testthat/test-is_converged_stan.R |only tests/testthat/test-iv_robust.R | 3 tests/testthat/test-lavaan.R | 50 + tests/testthat/test-lme.R | 669 +++++++++++++++++++++++ tests/testthat/test-merModList.R |only tests/testthat/test-mmrm.R | 2 tests/testthat/test-n_obs_brms.R |only tests/testthat/test-null_model.R | 59 ++ 83 files changed, 5636 insertions(+), 593 deletions(-)
Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between contfrac versions 1.1-12 dated 2018-05-17 and 1.1-13 dated 2026-10-13
contfrac-1.1-12/contfrac/tests/aaa.R |only contfrac-1.1-13/contfrac/DESCRIPTION | 20 +++++++++++---- contfrac-1.1-13/contfrac/MD5 | 23 +++++++++++++---- contfrac-1.1-13/contfrac/R/contfrac.R | 30 +++++++++++++++++++---- contfrac-1.1-13/contfrac/README.md |only contfrac-1.1-13/contfrac/build |only contfrac-1.1-13/contfrac/inst |only contfrac-1.1-13/contfrac/man/CF.Rd | 8 +++--- contfrac-1.1-13/contfrac/man/contfrac-package.Rd |only contfrac-1.1-13/contfrac/man/convergents.Rd | 16 ++++++++++-- contfrac-1.1-13/contfrac/man/figures |only contfrac-1.1-13/contfrac/src/contfrac.c | 20 +++++++-------- contfrac-1.1-13/contfrac/tests/testthat |only contfrac-1.1-13/contfrac/tests/testthat.R |only contfrac-1.1-13/contfrac/vignettes |only 15 files changed, 85 insertions(+), 32 deletions(-)
Title: Direction-Aware Sufficient Condition Analysis
Description: Tests whether a high or low level of a condition is enough to
guarantee a high or low level of an outcome. Such a claim predicts that one
corner of the condition-outcome scatter plot is empty of observations. The
package estimates the boundary of that empty corner, its size as a share of
the scope (the effect size), a permutation test against random pairing, and
a threshold table giving the condition level that guarantees each outcome
level, in actual units, percentages, percentiles or standard deviations.
Each of the four directions (high or low condition, high or low outcome) is
stated as a claim and mapped to its empty corner. Because a condition can
rule out low outcomes while barely moving the average, results can be set
beside ordinary least-squares and median regression slopes, showing whether
the data hold an average effect, a sufficiency effect or both. Also
provides plots, influential-case diagnostics, scope-sensitivity and
resampling checks, random-data generation and power [...truncated...]
Author: Young Chan [aut, cre]
Maintainer: Young Chan <youngchanresearcher@gmail.com>
Diff between SCAtools versions 0.4.3 dated 2026-09-18 and 0.5.1 dated 2026-10-13
SCAtools-0.4.3/SCAtools/man/sca_corners.Rd |only SCAtools-0.4.3/SCAtools/man/sca_diagnostics.Rd |only SCAtools-0.4.3/SCAtools/man/sca_plots.Rd |only SCAtools-0.4.3/SCAtools/man/sca_results.Rd |only SCAtools-0.5.1/SCAtools/DESCRIPTION | 44 SCAtools-0.5.1/SCAtools/MD5 | 94 SCAtools-0.5.1/SCAtools/NAMESPACE | 23 SCAtools-0.5.1/SCAtools/NEWS.md | 1046 +++++++++ SCAtools-0.5.1/SCAtools/R/SCAtools-package.R |only SCAtools-0.5.1/SCAtools/R/analysis.R | 977 ++++++++ SCAtools-0.5.1/SCAtools/R/compare.R |only SCAtools-0.5.1/SCAtools/R/corners.R | 223 +- SCAtools-0.5.1/SCAtools/R/data.R |only SCAtools-0.5.1/SCAtools/R/diagnostics.R | 230 +- SCAtools-0.5.1/SCAtools/R/magnitude.R |only SCAtools-0.5.1/SCAtools/R/plots.R | 204 + SCAtools-0.5.1/SCAtools/R/resample.R |only SCAtools-0.5.1/SCAtools/R/results.R | 1110 +++++++++- SCAtools-0.5.1/SCAtools/R/scales.R | 52 SCAtools-0.5.1/SCAtools/R/simulation.R | 91 SCAtools-0.5.1/SCAtools/README.md | 291 +- SCAtools-0.5.1/SCAtools/build |only SCAtools-0.5.1/SCAtools/data |only SCAtools-0.5.1/SCAtools/inst/CITATION | 24 SCAtools-0.5.1/SCAtools/inst/NOTICE | 2 SCAtools-0.5.1/SCAtools/inst/docs/README_zh-TW.md | 253 -- SCAtools-0.5.1/SCAtools/inst/docs/sufficiency-logic.md | 7 SCAtools-0.5.1/SCAtools/inst/extdata |only SCAtools-0.5.1/SCAtools/man/SCAtools-package.Rd | 128 + SCAtools-0.5.1/SCAtools/man/sca.Rd |only SCAtools-0.5.1/SCAtools/man/sca_analysis.Rd | 212 + SCAtools-0.5.1/SCAtools/man/sca_boundary_type.Rd |only SCAtools-0.5.1/SCAtools/man/sca_check_direction.Rd |only SCAtools-0.5.1/SCAtools/man/sca_compare.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner_location.Rd |only SCAtools-0.5.1/SCAtools/man/sca_corner_map.Rd |only SCAtools-0.5.1/SCAtools/man/sca_direction.Rd |only SCAtools-0.5.1/SCAtools/man/sca_empty_space.Rd |only SCAtools-0.5.1/SCAtools/man/sca_extract.Rd |only SCAtools-0.5.1/SCAtools/man/sca_four_configurations.Rd |only SCAtools-0.5.1/SCAtools/man/sca_legacy_names.Rd |only SCAtools-0.5.1/SCAtools/man/sca_locationshift.Rd |only SCAtools-0.5.1/SCAtools/man/sca_magnitude.Rd |only SCAtools-0.5.1/SCAtools/man/sca_normalize.Rd |only SCAtools-0.5.1/SCAtools/man/sca_outliers.Rd |only SCAtools-0.5.1/SCAtools/man/sca_output.Rd |only SCAtools-0.5.1/SCAtools/man/sca_plot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_power.Rd | 100 SCAtools-0.5.1/SCAtools/man/sca_powerplot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_random.Rd | 50 SCAtools-0.5.1/SCAtools/man/sca_reference.Rd | 86 SCAtools-0.5.1/SCAtools/man/sca_relationship.Rd |only SCAtools-0.5.1/SCAtools/man/sca_resample.Rd |only SCAtools-0.5.1/SCAtools/man/sca_rescale.Rd |only SCAtools-0.5.1/SCAtools/man/sca_scales.Rd | 72 SCAtools-0.5.1/SCAtools/man/sca_scope.Rd |only SCAtools-0.5.1/SCAtools/man/sca_scope_sensitivity.Rd |only SCAtools-0.5.1/SCAtools/man/sca_table.Rd |only SCAtools-0.5.1/SCAtools/man/sca_terms.Rd |only SCAtools-0.5.1/SCAtools/man/sca_test_plot.Rd |only SCAtools-0.5.1/SCAtools/man/sca_thresholds.Rd |only SCAtools-0.5.1/SCAtools/tests/testthat/test-adjust-resample.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-analysis.R | 54 SCAtools-0.5.1/SCAtools/tests/testthat/test-api-0-5-0.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-configurations.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-magnitude.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-refusals.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-scope.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-settings.R |only SCAtools-0.5.1/SCAtools/tests/testthat/test-simulation.R | 40 SCAtools-0.5.1/SCAtools/tests/testthat/test-symmetry.R |only 72 files changed, 4455 insertions(+), 958 deletions(-)
Title: Fast Interactive Data Analysis Pipelines
Description: A lightweight and intuitive framework for building interactive data
analysis pipelines. You add R functions one by one, and 'pipeflow'
wires them into a pipeline that stays consistent as you go. Modify,
remove, or insert steps at any stage, manage all parameters in one
place, fast execution (C++-powered DAG) for interactive use and Shiny
backends.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between pipeflow versions 0.4.0 dated 2026-09-27 and 0.5.0 dated 2026-10-13
DESCRIPTION | 10 LICENSE | 4 MD5 | 126 + NAMESPACE | 4 NEWS.md | 76 + R/RcppExports.R | 8 R/generic.pipeflow.R | 52 R/log.R | 38 R/pipeflow-package.R | 11 R/pipeflow.R | 1114 +++++++++++++---- R/print.pipeflow.R | 71 + R/utils.R | 51 build/vignette.rds |binary inst/doc/v01-get-started.R | 26 inst/doc/v01-get-started.Rmd | 54 inst/doc/v01-get-started.html | 177 +- inst/doc/v02-modify-pipeline.html | 34 inst/doc/v03a-combine-pipelines.R | 19 inst/doc/v03a-combine-pipelines.Rmd | 42 inst/doc/v03a-combine-pipelines.html | 124 + inst/doc/v03b-pipeline-views.R | 46 inst/doc/v03b-pipeline-views.Rmd | 73 - inst/doc/v03b-pipeline-views.html | 206 ++- inst/doc/v04-collect-output.R | 8 inst/doc/v04-collect-output.Rmd | 8 inst/doc/v04-collect-output.html | 27 inst/doc/v05a-split-map-reduce.html | 85 - inst/doc/v05b-nested-pipeline.R | 2 inst/doc/v05b-nested-pipeline.Rmd | 28 inst/doc/v05b-nested-pipeline.html | 145 +- inst/doc/v05c-error-handling.R |only inst/doc/v05c-error-handling.Rmd |only inst/doc/v05c-error-handling.html |only inst/doc/v05d-param-value.R |only inst/doc/v05d-param-value.Rmd |only inst/doc/v05d-param-value.html |only inst/doc/v06-self-modify-pipeline.Rmd | 8 inst/doc/v06-self-modify-pipeline.html | 121 + man/Extract.pipeflow.Rd | 18 man/pip_add.Rd | 27 man/pip_new.Rd | 20 man/pip_param_value.Rd |only man/pip_remove.Rd | 21 man/pip_replace.Rd | 52 man/pip_run.Rd | 117 + man/pip_run_state.Rd |only man/pip_set_params.Rd | 51 man/pip_view.Rd | 11 man/pipeflow_lgr.Rd |only man/print.Rd | 8 src/RcppExports.cpp | 27 src/dag.cpp | 161 ++ tests/testthat/helper_dag.R | 25 tests/testthat/helper_general.R | 10 tests/testthat/test_RcppExports.R | 124 + tests/testthat/test_generic.pipeflow.R | 240 +++ tests/testthat/test_log.R | 92 + tests/testthat/test_pipeflow.R | 2107 ++++++++++++++++++++++++++++++++- tests/testthat/test_print.pipeflow.R | 176 ++ tests/testthat/test_utils.R | 31 vignettes/articles/v07-vs-targets.Rmd | 996 +++++++++++---- vignettes/articles/v07-vs-targets.html |only vignettes/v01-get-started.Rmd | 54 vignettes/v03a-combine-pipelines.Rmd | 42 vignettes/v03b-pipeline-views.Rmd | 73 - vignettes/v04-collect-output.Rmd | 8 vignettes/v05b-nested-pipeline.Rmd | 28 vignettes/v05c-error-handling.Rmd |only vignettes/v05d-param-value.Rmd |only vignettes/v06-self-modify-pipeline.Rmd | 8 70 files changed, 6086 insertions(+), 1239 deletions(-)
Title: Modelling Reproduction and Survival Data in Ecotoxicology
Description: Advanced methods for a valuable quantitative environmental risk
assessment using Bayesian inference of survival and reproduction Data. Among
others, it facilitates Bayesian inference of the general unified
threshold model of survival (GUTS). See our companion paper
Baudrot and Charles (2021) <doi:10.21105/joss.03200>,
as well as complementary details in Baudrot et al. (2018)
<doi:10.1021/acs.est.7b05464> and Delignette-Muller et al.
(2017) <doi:10.1021/acs.est.6b05326>.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Nils Kehrein [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [ctb],
Alexander Singer [ [...truncated...]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between morse versions 3.3.5 dated 2026-01-14 and 3.6.0 dated 2026-10-13
DESCRIPTION | 16 +++--- MD5 | 46 ++++++++++--------- NAMESPACE | 2 NEWS | 6 ++ R/morse-internal.R | 19 ++++++++ R/morse.R | 2 R/plot.reproFitTT.R | 1 R/plotDoseResponse.reproData.R | 9 +-- R/plot_prior_post.R | 2 R/predict_Nsurv_check.R | 2 R/priors_distribution.R | 2 R/summary.survFit.R | 2 build/partial.rdb |only inst/doc/MinimalWorkingExample.html | 3 - inst/doc/modelling.html | 2 inst/doc/tutorial.html | 84 +++++++++++++++++------------------- man/morse-package.Rd | 2 man/plotDoseResponse.reproData.Rd | 7 --- man/plot_prior_post.survFit.Rd | 2 man/predict_check.Rd | 2 man/priors_distribution.survFit.Rd | 2 man/summary.survFit.Rd | 2 tests/testthat/test-LCx.R | 4 - tests/testthat/test-surv.R | 74 +++++++++++++++++++++++++++++++ tests/testthat/test-survFit.R |only 25 files changed, 188 insertions(+), 105 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-03 0.1
Title: Statistical Matching Using Latent Class Models
Description: Provides a revised framework (1.2->2.0) for statistical matching of categorical data based on latent class models, including multiple imputation, predictive modeling, nearest-neighbour hot-deck matching, and probabilistic assignment of categorical target variables. It allows researchers to perform data integration when no unique identifiers are available by modeling the joint distribution of variables through latent categorical structures. The package supports estimation of latent class models, probabilistic matching between donor and recipient data sets, and generation of synthetic linked data under uncertainty. It is particularly useful in survey research and data fusion applications where combining information from multiple sources is required while preserving statistical properties and accounting for measurement error and missing data mechanisms.
Author: Alicja Wolny-Dominiak [aut, cre],
Israa Lewaaelhamd [aut],
Mohammed Ali Ismail [aut]
Maintainer: Alicja Wolny-Dominiak <woali@ue.katowice.pl>
Diff between statMatchLCM versions 1.2 dated 2026-05-15 and 2.0 dated 2026-10-13
DESCRIPTION | 8 MD5 | 40 NAMESPACE | 2 R/statMatchLCM.R | 2185 +++++++++++++++++++++++++++++----------------------- R/zzz.R |only data/datA.rda |binary data/datB.rda |binary data/datC.rda |only man/datA.Rd | 4 man/datABC_to_SM.Rd |only man/datAB_to_SM.Rd | 10 man/datB.Rd | 6 man/datC.Rd |only man/num_to_fact.Rd | 14 man/sm_quality.Rd | 8 man/sma1_step2.Rd | 14 man/sma2_step2.Rd | 22 man/sma3_step2.Rd | 23 man/sma_step1.Rd | 32 man/smc1_step2.Rd | 6 man/smc2_step2.Rd | 10 man/smc3_step2.Rd | 9 man/smc_step1.Rd | 20 23 files changed, 1339 insertions(+), 1074 deletions(-)
Title: Package Checks for 'rOpenSci'
Description: Check whether a package is ready for submission to the 'rOpenSci'
peer review system ('rOpenSci' authors (2026) <doi:10.5281/zenodo.2553043>
"'rOpenSci' Packages: Development, Maintenance, and Peer Review").
Incorporates the 'goodpractice' package and many additional checks,
including aspects related to maintenance of online public code
repositories.
Author: Mark Padgham [aut, cre] ,
Maelle Salmon [aut],
Jacob Wujciak-Jens [aut] ,
Kelli F. Johnson [ctb] ,
Eunseop Kim [aut] ,
Katrina Brock [ctb] ,
Andy Teucher [aut] ,
Eric R. Scott [aut]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgcheck versions 0.3.3 dated 2026-10-06 and 0.3.4 dated 2026-10-13
DESCRIPTION | 6 - MD5 | 60 +++++++++-------- NEWS.md | 10 ++ R/info-ci.R | 3 R/info-git.R | 3 R/info-github.R | 4 - R/pkgcheck-info.R | 3 R/stats-checks.R | 65 +++++++++++-------- R/utils.R | 16 ++++ inst/doc/autotest-pkgcheck-gp.html | 6 - inst/doc/environment.html | 6 - inst/doc/extending-checks.html | 6 - inst/doc/list-checks.html | 6 - tests/testthat/_snaps/extra-checks/checks-extra.html | 50 +++++++------- tests/testthat/_snaps/extra-checks/checks-extra.md | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks0.html | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks0.md | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks1.html | 50 +++++++------- tests/testthat/_snaps/pkgcheck/checks1.md | 50 +++++++------- tests/testthat/helper-check-data.R | 17 +++- tests/testthat/test-cache.R | 5 + tests/testthat/test-check-ci.R | 8 +- tests/testthat/test-check-left-assign.R | 2 tests/testthat/test-check-scrap.R | 8 ++ tests/testthat/test-extra-checks.R | 11 +-- tests/testthat/test-extra-env-check.R | 4 - tests/testthat/test-goodpractice.R | 2 tests/testthat/test-pkgcheck.R | 5 - tests/testthat/test-pkgcheck_bg.R | 4 - vignettes/autotest-pkgcheck-gp.md |only vignettes/environment.md |only vignettes/extending-checks.md |only vignettes/list-checks.md |only 33 files changed, 312 insertions(+), 248 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests for independent groups designs under homoscedasticity and heteroscedasticity. The tests described by Dag et al. (2018) <doi:10.32614/RJ-2018-022> include one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second-order test, and Kruskal-Wallis test. Additional tests described by Kasikci et al. (2026) <doi:10.32614/RJ-2026-014> include Scott-Smith test, Box F test, Johansen F test, generalized tests equivalent to parametric bootstrap and fiducial tests, Alvandi's F test, Alvandi's generalized p-value, approximate F test, B square test, Cochran test, Weerahandi's generalized F test, modified Brown-Forsythe test, adjusted Welch's heteroscedastic F test, Welch-Aspin test, and permutation F test. The package also provides pairwise comparisons and graphical methods, as well as Student's t test, Welch's t test, and M [...truncated...]
Author: Osman Dag [aut, cre],
Merve Kasikci [aut],
Anil Dolgun [aut],
N. Meric Konar [aut],
Sam Weerahandi [aut],
Malwane Ananda [aut],
H. Erkin Sulekli [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 3.1 dated 2025-07-22 and 3.2 dated 2026-10-13
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- inst/citation | 50 ++++++++++++++++++++++++++++++++++---------------- 3 files changed, 43 insertions(+), 25 deletions(-)
Title: Technology Appraisal Toolbox for Health Economic Evaluations in
the Netherlands
Description: Functions to support economic modelling in R based on the methods of the
Dutch guideline for economic evaluations in healthcare <https://www.zorginstituutnederland.nl/documenten/2024/01/16/richtlijn-voor-het-uitvoeren-van-economische-evaluaties-in-de-gezondheidszorg>,
CBS data <https://www.cbs.nl/>, and OECD data <https://www.oecd.org/en.html>.
Author: Stijn Peeters [aut, cre] ,
Eline Krijkamp [aut] ,
Frederick Thielen [aut]
Maintainer: Stijn Peeters <s.b.peeters@eshpm.eur.nl>
Diff between tatooheene versions 1.0.0 dated 2025-12-15 and 1.0.1 dated 2026-10-13
DESCRIPTION | 8 - MD5 | 44 ++++--- R/apply_discounting.R | 2 R/globals.R | 43 +++---- R/nl_ppp.R | 72 ++++++------ R/nl_price_index.R | 185 ++++++++++++++++--------------- R/nl_ref_prices.R | 34 ++++- build/vignette.rds |binary data/df_cpi_combined.rda |binary data/df_fp.rda |binary data/df_ppp.rda |binary data/df_ref_prices.rda |binary inst/doc/apply-discounting.html | 142 +++++++++++------------- inst/doc/depreciation-interest.R | 2 inst/doc/depreciation-interest.html | 10 + inst/doc/friction-period.html | 11 + inst/doc/getting-started.R | 44 +++---- inst/doc/getting-started.html | 3 inst/doc/nl-ref-prices.html | 188 +++++++++++++++++++++++++++++--- man/nl_price_index.Rd | 1 tests/testthat/test-apply_discounting.R |only tests/testthat/test-nl_ppp.R |only tests/testthat/test-nl_price_index.R | 7 + tests/testthat/test-nl_ref_prices.R |only tests/testthat/test-pretty_price.R |only 25 files changed, 505 insertions(+), 291 deletions(-)
Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>. The software itself
is introduced in Feng, Y., Gries, T., Letmathe, S., and Schulz, D. (2022)
<doi:10.32614/RJ-2022-017>.
Author: Yuanhua Feng [aut] ,
Sebastian Letmathe [aut] ,
Dominik Schulz [aut, cre] ,
Thomas Gries [ctb] ,
Marlon Fritz [ctb]
Maintainer: Dominik Schulz <dominik.schulz.r@gmail.com>
Diff between smoots versions 1.1.4 dated 2023-09-11 and 1.1.5 dated 2026-10-13
smoots-1.1.4/smoots/man/smoots.Rd |only smoots-1.1.5/smoots/DESCRIPTION | 30 +-- smoots-1.1.5/smoots/MD5 | 101 ++++++------- smoots-1.1.5/smoots/NAMESPACE | 52 ++++-- smoots-1.1.5/smoots/NEWS.md | 14 + smoots-1.1.5/smoots/R/Welcome.R | 2 smoots-1.1.5/smoots/R/algorithms.R | 5 smoots-1.1.5/smoots/R/bootCast.R | 25 +-- smoots-1.1.5/smoots/R/cf0.LW.est.R | 42 +++-- smoots-1.1.5/smoots/R/confBounds.R | 13 - smoots-1.1.5/smoots/R/critMatrix.R | 2 smoots-1.1.5/smoots/R/dsmooth.R | 13 - smoots-1.1.5/smoots/R/fitted.R | 2 smoots-1.1.5/smoots/R/gsmooth.R | 3 smoots-1.1.5/smoots/R/knsmooth.R | 3 smoots-1.1.5/smoots/R/modelCast.R | 17 +- smoots-1.1.5/smoots/R/msmooth.R | 31 ++- smoots-1.1.5/smoots/R/msmoothCalc.R | 6 smoots-1.1.5/smoots/R/normCast.R | 12 - smoots-1.1.5/smoots/R/optOrd.R | 2 smoots-1.1.5/smoots/R/plot.smoots.R | 2 smoots-1.1.5/smoots/R/print.smoots.R | 2 smoots-1.1.5/smoots/R/rescale.R | 2 smoots-1.1.5/smoots/R/residuals.R | 2 smoots-1.1.5/smoots/R/rollCast.R | 7 smoots-1.1.5/smoots/R/smoots.R | 14 - smoots-1.1.5/smoots/R/trendCast.R | 3 smoots-1.1.5/smoots/R/tsmooth.R | 34 +++- smoots-1.1.5/smoots/R/tsmoothCalc.R | 27 ++- smoots-1.1.5/smoots/README.md | 59 ++++--- smoots-1.1.5/smoots/inst |only smoots-1.1.5/smoots/man/bootCast.Rd | 16 +- smoots-1.1.5/smoots/man/confBounds.Rd | 13 - smoots-1.1.5/smoots/man/critMatrix.Rd | 2 smoots-1.1.5/smoots/man/dsmooth.Rd | 13 - smoots-1.1.5/smoots/man/figures/logo_smoots.png |only smoots-1.1.5/smoots/man/fitted.smoots.Rd | 2 smoots-1.1.5/smoots/man/gsmooth.Rd | 3 smoots-1.1.5/smoots/man/knsmooth.Rd | 3 smoots-1.1.5/smoots/man/modelCast.Rd | 17 +- smoots-1.1.5/smoots/man/msmooth.Rd | 30 ++- smoots-1.1.5/smoots/man/normCast.Rd | 12 - smoots-1.1.5/smoots/man/optOrd.Rd | 2 smoots-1.1.5/smoots/man/plot.smoots.Rd | 2 smoots-1.1.5/smoots/man/print.smoots.Rd | 2 smoots-1.1.5/smoots/man/rescale.Rd | 2 smoots-1.1.5/smoots/man/residuals.smoots.Rd | 2 smoots-1.1.5/smoots/man/rollCast.Rd | 7 smoots-1.1.5/smoots/man/smoots-package.Rd |only smoots-1.1.5/smoots/man/trendCast.Rd | 3 smoots-1.1.5/smoots/man/tsmooth.Rd | 30 ++- smoots-1.1.5/smoots/src/gsmoothCpp.cpp | 8 - smoots-1.1.5/smoots/tests/testthat/test_cores_number.R |only smoots-1.1.5/smoots/tests/testthat/test_smoots_algorithm.R | 2 54 files changed, 401 insertions(+), 297 deletions(-)
Title: Parameter Space Partitioning MCMC for Global Model Evaluation
Description: Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.
Author: Lenard Dome [aut, cre],
Andy Wills [aut]
Maintainer: Lenard Dome <lenarddome@gmail.com>
Diff between psp versions 1.0.5 dated 2026-01-15 and 1.0.6 dated 2026-10-13
DESCRIPTION | 11 MD5 | 15 - NEWS.md |only build/partial.rdb |binary man/figures |only man/pspGlobal.Rd | 2 src/pspGlobal.cpp | 417 +++++++++++++++----------------- tests/testthat/helper-models.R |only tests/testthat/test_psp_cpp.R | 4 tests/testthat/test_psp_cpp_callbacks.R |only tests/testthat/test_psp_cpp_sampler.R |only 11 files changed, 223 insertions(+), 226 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut] ,
Nicolas Lambert [aut] ,
Timothee Giraud [aut, cre]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.6.0 dated 2023-10-31 and 0.7.0 dated 2026-10-13
MTA-0.6.0/MTA/NEWS |only MTA-0.7.0/MTA/DESCRIPTION | 20 MTA-0.7.0/MTA/MD5 | 44 MTA-0.7.0/MTA/NAMESPACE | 18 MTA-0.7.0/MTA/NEWS.md |only MTA-0.7.0/MTA/R/gdev.R | 2 MTA-0.7.0/MTA/R/package.R | 16 MTA-0.7.0/MTA/R/tdev.R | 2 MTA-0.7.0/MTA/README.md | 22 MTA-0.7.0/MTA/build/vignette.rds |binary MTA-0.7.0/MTA/inst/doc/MTA.Rmd | 6 MTA-0.7.0/MTA/inst/doc/MTA.html | 172 +-- MTA-0.7.0/MTA/inst/doc/MTA_Scenario.R | 56 - MTA-0.7.0/MTA/inst/doc/MTA_Scenario.Rmd | 72 - MTA-0.7.0/MTA/inst/doc/MTA_Scenario.html | 1429 +++++++++++++++---------------- MTA-0.7.0/MTA/man/MTA.Rd | 12 MTA-0.7.0/MTA/man/cardist.Rd | 4 MTA-0.7.0/MTA/man/com.Rd | 4 MTA-0.7.0/MTA/man/ept.Rd | 4 MTA-0.7.0/MTA/man/gdev.Rd | 2 MTA-0.7.0/MTA/man/tdev.Rd | 2 MTA-0.7.0/MTA/vignettes/MTA.Rmd | 6 MTA-0.7.0/MTA/vignettes/MTA_Scenario.Rmd | 72 - MTA-0.7.0/MTA/vignettes/mta.bib | 31 24 files changed, 1027 insertions(+), 969 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.8-3 dated 2026-10-06 and 1.8-4 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/dpq_etc.R | 4 ++-- R/mmlt.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++++++++ tests/bugfixes.R | 6 ++++++ tests/bugfixes.Rout.save | 12 ++++++++++-- 8 files changed, 39 insertions(+), 15 deletions(-)
Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between cpop versions 1.0.9 dated 2026-05-29 and 1.0.10 dated 2026-10-13
DESCRIPTION | 16 +- MD5 | 36 ++-- NAMESPACE | 13 + NEWS.md | 7 R/cpop.R | 14 + R/cpop.crops.R | 284 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/stage23.rdb |binary man/changepoints-methods.Rd | 3 man/cost-methods.Rd | 3 man/cpop.crops-methods.Rd | 2 man/cpop.crops.models-methods.Rd | 2 man/estimate-methods.Rd | 3 man/plot-methods.Rd | 23 ++- man/print-methods.Rd |only man/segmentations-methods.Rd |only man/show-methods.Rd | 3 man/subset-methods.Rd |only man/summary-methods.Rd | 14 + man/unique-methods.Rd |only src/prune.impl.cpp | 2 21 files changed, 385 insertions(+), 40 deletions(-)
Title: Predict and Map Oyster Growth Suitability from Environmental
Data
Description: Predicts spatial suitability for oyster growth from environmental
survey data using rank-reciprocal weighted scoring.
Users supply sensor data from Acoustic Doppler Current Profilers (ADCP),
Conductivity-Temperature-Depth (CTD) sensors, bathymetric sonar, and
sidescan sonar, specify a target species, and receive per-location
suitability scores, a five-band 'GeoTIFF' heatmap for 'QGIS', contour
lines, and a formatted PDF or HTML report. Supports seventeen species across
global aquaculture regions, including Ostrea edulis, Magallana gigas,
Crassostrea virginica, Crassostrea hongkongensis, and thirteen further
species; see list_species(). Includes ocean acidification scoring via
in-house aragonite saturation state (Omega_arag) calculation using
Lueker et al. (2000) <doi:10.1016/S0304-4203(00)00022-0> and Mucci (1983)
<doi:10.1357/002224083788520153> equilibrium constants (no external
dependencies), variable impact diagnostics (variable_impact()), fine-scale
habitat area analys [...truncated...]
Author: T Tucker [aut, cre]
Maintainer: T Tucker <tristantucker48@gmail.com>
Diff between oystermapR versions 1.5.0 dated 2026-08-31 and 1.6.0 dated 2026-10-13
DESCRIPTION | 20 +- MD5 | 88 ++++++---- NAMESPACE | 20 ++ NEWS.md | 173 +++++++++++++++++++ R/area_summary.R | 31 ++- R/bayesian_update.R | 207 +++++++++++++++-------- R/evidence_weights.R |only R/exclusion_check.R | 43 ++-- R/export_geotiff.R | 107 +++++++++++- R/help.R | 144 +++++++++++++++- R/layer_reproducibility.R |only R/lineage_tolerances.R |only R/oystermapR-package.R | 2 R/predict_oyster.R | 244 +++++++++++++++++++++++++++- R/species_tolerances.R | 2 R/summary_pdf.R | 64 +++++-- R/validate.R | 4 R/variable_importance.R | 2 README.md | 67 +++++++ inst/REFERENCES.md | 4 inst/doc/example-bay-survey.R | 47 +++++ inst/doc/example-bay-survey.Rmd | 172 ++++++++++++++++++- inst/doc/example-bay-survey.html | 170 ++++++++++++++++++- inst/rmd/oystermapR_report.Rmd | 2 man/area_summary.Rd | 15 + man/as_lineage_distances.Rd |only man/confidence_score.Rd |only man/dot-apply_evidence_weighting.Rd |only man/dot-evidence_row_support.Rd |only man/dot-fit_suitability.Rd |only man/dot-params_at.Rd |only man/evidence_coverage.Rd |only man/evidence_suitability.Rd |only man/evidence_weights.Rd |only man/export_contours.Rd | 3 man/export_geotiff.Rd | 19 +- man/export_qml_style.Rd | 10 + man/fit_lineages.Rd |only man/layer_reproducibility.Rd |only man/lineage_fits_as_list.Rd |only man/lineage_occurrence.Rd |only man/lineage_signal.Rd |only man/oystermapR-package.Rd | 2 man/oystermapR_help.Rd | 5 man/predict_oyster.Rd | 88 +++++++++- man/rank_source_populations.Rd |only man/reliability_from_perturbation.Rd |only man/reliability_from_replicates.Rd |only man/update_species_tolerances.Rd | 24 ++ man/validate_against_records.Rd | 2 man/weight_table_md.Rd |only tests/testthat/test-bayesian.R | 84 +++++++++ tests/testthat/test-core.R | 65 +++++++ tests/testthat/test-evidence-weights.R |only tests/testthat/test-layer-reproducibility.R |only tests/testthat/test-lineage-tolerances.R |only vignettes/example-bay-survey.Rmd | 172 ++++++++++++++++++- 57 files changed, 1874 insertions(+), 228 deletions(-)
Title: Fitting the Metastatistical Extreme Value Distribution MEVD
Description: Extreme value analysis with the metastatistical extreme value distribution MEVD (Marani and Ignaccolo, 2015, <doi:10.1016/j.advwatres.2015.03.001>) and some of its variants. In particular, analysis can be performed with the simplified metastatistical extreme value distribution SMEV (Marra et al., 2019, <doi:10.1016/j.advwatres.2019.04.002>) and the temporal metastatistical extreme value distribution TMEV (Falkensteiner et al., 2023, <doi:10.1016/j.wace.2023.100601>). Parameters can be estimated with probability weighted moments, maximum likelihood and least squares. The data can also be left-censored prior to a fit. Density, distribution function, quantile function and random generation for the MEVD, SMEV and TMEV are included. In addition, functions for the calculation of return levels including confidence intervals are provided. For a description of use cases please see the provided references.
Author: Harald Schellander [aut, cre] ,
Alexander Lieb [ctb] ,
Marc-Andre Falkensteiner [ctb]
Maintainer: Harald Schellander <harald.schellander@geosphere.at>
Diff between mevr versions 1.1.1 dated 2024-06-30 and 1.3.3 dated 2026-10-13
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 88 - NEWS | 84 - R/mevr.R | 2651 ++++++++++++++++++++++---------- R/weibull_tail_test.R | 263 +-- README.md | 10 build |only man/censored_weibull_fit.Rd | 15 man/dailyrainfall.Rd | 20 man/dmev.Rd | 22 man/dtmev.Rd | 19 man/event_separation.Rd |only man/fmev.Rd | 170 +- man/fsmev.Rd | 209 +- man/ftmev.Rd | 207 +- man/ordinary_events.Rd |only man/plot.mevr.Rd | 24 man/pp.weibull.Rd | 9 man/predict.mevr.Rd | 40 man/return.levels.mev.Rd | 29 man/weibull_tail_test.Rd | 70 tests/testthat/test-dtmev.R | 44 tests/testthat/test-event_separation.R |only tests/testthat/test-fmev.R | 183 +- tests/testthat/test-fsmev.R | 344 ++-- tests/testthat/test-ftmev.R | 147 + tests/testthat/test-left-censoring.R |only tests/testthat/test-ordinary_events.R |only tests/testthat/test-pp-weibull.R | 12 tests/testthat/test-predict-mevr.R | 85 - tests/testthat/test-print-mevr.R | 150 + tests/testthat/test-qtmev.R | 8 tests/testthat/test-return-levels-mev.R | 173 +- tests/testthat/test-return-levels.R | 222 +- tests/testthat/test-weibull-tail-test.R | 119 - 36 files changed, 3618 insertions(+), 1881 deletions(-)
Title: Chinese Text Segmentation, POS Tagging, and Keyword Extraction
Description: Provides fast Chinese text segmentation, keyword extraction
via 'TF-IDF' and 'TextRank', and part-of-speech tagging, powered by a
'Rust' backend ('jieba-rs'). Supports custom dictionaries, user words,
stop words, IDF files, and HMM models, with parallel batch processing
of multiple strings. Serves as a modern, maintained replacement for
the 'jiebaR' package.
Author: Hao Cheng [aut, cre, cph]
Maintainer: Hao Cheng <Yousa-Mirage@foxmail.com>
Diff between jiebaRS versions 0.3.0 dated 2026-08-26 and 0.3.1 dated 2026-10-13
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 5 + README.md | 10 +-- inst/WORDLIST | 2 src/rust/Cargo.lock | 147 +------------------------------------------------ src/rust/Cargo.toml | 2 src/rust/vendor.tar.xz |binary 8 files changed, 25 insertions(+), 161 deletions(-)
Title: Geometric Features and Footprint Comparison for 'sf' Objects
Description: Extracts reproducible geometric and urban-morphology descriptors from
polygon and multipart polygon building footprints stored as 'sf' objects,
including area, perimeter, compactness, shape, topology, convexity, orientation,
and optional building-height and floor-area metrics. Compares polygon footprints
across periods using the intersection-over-union (Jaccard) index (Jaccard,
1912) <doi:10.1111/j.1469-8137.1912.tb05611.x> to identify new constructions,
potential demolitions, and footprint changes. Supports vector file formats
readable by 'sf', including Shapefiles and GeoPackage (GPKG) vector files with
named layers, optional boundary clipping, and reprojection to a common coordinate
reference system. Returned 'sf' objects preserve source attributes and geometry
for spatial analysis and downstream workflows, with optional parallel processing
using 'future' for larger feature-extraction jobs.
Author: Jonathan Cohen [aut, cre]
Maintainer: Jonathan Cohen <cohen.jota@gmail.com>
Diff between geomorphR versions 0.1.0 dated 2026-10-04 and 0.2.0 dated 2026-10-13
DESCRIPTION | 21 ++- MD5 | 27 ++++ NAMESPACE | 1 NEWS.md |only R/compare_footprints.R |only README.md | 130 +++++++++++++++++++++-- inst/examples |only inst/extdata/footprint_comparison |only man/compare_footprints.Rd |only tests/testthat/test_compare_footprints.R |only tests/testthat/test_extract_geometric_features.R | 1 11 files changed, 162 insertions(+), 18 deletions(-)
Title: Genotyping Triploids/Tetraploids (or Diploids) from Luminescence
Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids and tetraploids.
Three main functions: Create_Dataset_from_file() to build dataset ; Clustering_parallele_from_dir() that regroups individuals with a same genotype based on proximity and
Genotyping_parallele_from_dir() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between GenoTriplo versions 2.2.1 dated 2026-07-28 and 2.2.2 dated 2026-10-13
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- R/App_GenoTriploShiny.R | 37 +++++++++++++++++++++-------------- R/function_create_dataset.R | 2 - R/function_run_clustering.R | 8 +++++-- R/function_run_genotyping.R | 4 +-- man/Clustering_from_dir.Rd | 8 +++---- man/Create_Dataset_from_file.Rd | 2 - man/Genotyping_from_file.Rd | 2 - man/Genotyping_parallele_from_dir.Rd | 2 - 10 files changed, 51 insertions(+), 38 deletions(-)
Title: Continuous Epidemiological Week Indexing for Time-Series
Analysis
Description: Provides a simple algorithm to generate a continuous epidemiological week index from date variables in a data frame. Weeks are computed as sequential 7-day intervals aligned to Mondays, starting from the earliest observed date or from a user-supplied start date. They do not reset at calendar year boundaries and are not ISO 8601 nor MMWR calendar weeks. Missing or non-convertible dates are returned as NA instead of stopping the computation. The approach is intended for epidemiological modeling and time-series analysis where temporal continuity is required.
Author: Daniel Degina [aut, cre],
Joel Mbuyi [ctb]
Maintainer: Daniel Degina <deginadan@gmail.com>
Diff between cepiweek versions 0.1.2 dated 2026-02-19 and 0.2.0 dated 2026-10-13
DESCRIPTION | 14 +-- LICENSE | 4 MD5 | 16 +-- NAMESPACE | 6 - R/cepiweek.R | 165 +++++++++++++++++++++++++++-------------- README.md | 124 +++++++++++++++--------------- man/cepiweek.Rd | 141 +++++++++++++++++++---------------- tests/testthat.R | 107 +++++++++++++++++++++++--- tests/testthat/test-cepiweek.R | 118 +++++++++++++++++++++-------- 9 files changed, 456 insertions(+), 239 deletions(-)
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Francisco
Martinez et al. (2022) <doi:10.1016/j.neucom.2021.12.028>. When the forecasting
horizon is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.5 dated 2024-02-15 and 1.0.6 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/tsfgrnn.html | 48 +++++++++++++++++++++++++++++------------------- src/code.cpp | 6 +++--- 6 files changed, 46 insertions(+), 32 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 vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Brian Ripley [ctb],
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.7.1 dated 2026-09-29 and 5.1.8 dated 2026-10-13
rxode2-5.1.7.1/rxode2/src/linCmt.cpp |only rxode2-5.1.7.1/rxode2/src/linCmt.h |only rxode2-5.1.7.1/rxode2/src/linCmtDualN.h |only rxode2-5.1.7.1/rxode2/src/macros2micros.cpp |only rxode2-5.1.7.1/rxode2/src/macros2micros.h |only rxode2-5.1.7.1/rxode2/src/rxDerived.cpp |only rxode2-5.1.7.1/rxode2/src/rxode2_sundials_stan_compat.h |only rxode2-5.1.7.1/rxode2/src/solComp.cpp |only rxode2-5.1.7.1/rxode2/src/solComp.h |only rxode2-5.1.7.1/rxode2/tests/testthat/test-lincmt-modeldouble-senstype.R |only rxode2-5.1.8/rxode2/DESCRIPTION | 38 rxode2-5.1.8/rxode2/MD5 | 1156 rxode2-5.1.8/rxode2/NAMESPACE | 49 rxode2-5.1.8/rxode2/NEWS.md | 729 rxode2-5.1.8/rxode2/R/000.R | 6 rxode2-5.1.8/rxode2/R/CTS.R | 21 rxode2-5.1.8/rxode2/R/RcppExports.R | 89 rxode2-5.1.8/rxode2/R/adjoint.R | 995 rxode2-5.1.8/rxode2/R/adjointDiscrete.R | 536 rxode2-5.1.8/rxode2/R/asFunction.R | 16 rxode2-5.1.8/rxode2/R/asIni.R | 21 rxode2-5.1.8/rxode2/R/asModel.R | 33 rxode2-5.1.8/rxode2/R/asRxui.R | 18 rxode2-5.1.8/rxode2/R/assert.R | 697 rxode2-5.1.8/rxode2/R/build.R | 269 rxode2-5.1.8/rxode2/R/collectWarnings.R | 9 rxode2-5.1.8/rxode2/R/confint.R | 46 rxode2-5.1.8/rxode2/R/confintSummary.R | 89 rxode2-5.1.8/rxode2/R/d.R | 614 rxode2-5.1.8/rxode2/R/dde.R | 1166 rxode2-5.1.8/rxode2/R/dfIni.R | 222 rxode2-5.1.8/rxode2/R/dfWishart.R | 42 rxode2-5.1.8/rxode2/R/dsl.R | 317 rxode2-5.1.8/rxode2/R/elu.R | 48 rxode2-5.1.8/rxode2/R/err-foceiBase.R | 405 rxode2-5.1.8/rxode2/R/err-sim.R | 486 rxode2-5.1.8/rxode2/R/err.R | 1506 rxode2-5.1.8/rxode2/R/et-helpers.R | 475 rxode2-5.1.8/rxode2/R/et-methods.R | 263 rxode2-5.1.8/rxode2/R/et.R | 972 rxode2-5.1.8/rxode2/R/etNew.R | 499 rxode2-5.1.8/rxode2/R/etTran.R | 164 rxode2-5.1.8/rxode2/R/etVctrs.R | 37 rxode2-5.1.8/rxode2/R/etaDist.R |only rxode2-5.1.8/rxode2/R/eventSens.R | 633 rxode2-5.1.8/rxode2/R/evidPush.R | 89 rxode2-5.1.8/rxode2/R/fixef.R | 8 rxode2-5.1.8/rxode2/R/forder.R | 40 rxode2-5.1.8/rxode2/R/format.R | 18 rxode2-5.1.8/rxode2/R/gelu.R | 11 rxode2-5.1.8/rxode2/R/genShinyApp.template.R | 61 rxode2-5.1.8/rxode2/R/geom-amt.R | 17 rxode2-5.1.8/rxode2/R/geom-cens.R | 49 rxode2-5.1.8/rxode2/R/getBaseSim.R | 45 rxode2-5.1.8/rxode2/R/indLin.R | 146 rxode2-5.1.8/rxode2/R/intern.R | 47 rxode2-5.1.8/rxode2/R/linCmt.R | 160 rxode2-5.1.8/rxode2/R/linMod.R | 215 rxode2-5.1.8/rxode2/R/llik.R | 222 rxode2-5.1.8/rxode2/R/lotriCompat.R | 22 rxode2-5.1.8/rxode2/R/lrelu.R | 4 rxode2-5.1.8/rxode2/R/mix.R | 136 rxode2-5.1.8/rxode2/R/mlogit.R | 82 rxode2-5.1.8/rxode2/R/modelExtract.R | 198 rxode2-5.1.8/rxode2/R/modlib.R | 147 rxode2-5.1.8/rxode2/R/mu-cov-downgrade.R | 97 rxode2-5.1.8/rxode2/R/mu.R | 1011 rxode2-5.1.8/rxode2/R/normui.R |only rxode2-5.1.8/rxode2/R/odeToLin.R | 546 rxode2-5.1.8/rxode2/R/parseFuns.R | 64 rxode2-5.1.8/rxode2/R/piping-ini.R | 687 rxode2-5.1.8/rxode2/R/piping-model.R | 600 rxode2-5.1.8/rxode2/R/piping-update.R | 12 rxode2-5.1.8/rxode2/R/piping.R | 327 rxode2-5.1.8/rxode2/R/plogis.R | 12 rxode2-5.1.8/rxode2/R/plot.R | 201 rxode2-5.1.8/rxode2/R/prelu.R | 32 rxode2-5.1.8/rxode2/R/print.R | 234 rxode2-5.1.8/rxode2/R/prior-density-families.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels-cdf.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels.R |only rxode2-5.1.8/rxode2/R/prior-sim.R | 509 rxode2-5.1.8/rxode2/R/priorDensity.R | 447 rxode2-5.1.8/rxode2/R/progress.R | 2 rxode2-5.1.8/rxode2/R/rbind.R | 46 rxode2-5.1.8/rxode2/R/reexport.R | 1 rxode2-5.1.8/rxode2/R/relu.R | 4 rxode2-5.1.8/rxode2/R/rstudio.R | 12 rxode2-5.1.8/rxode2/R/rudf.R | 557 rxode2-5.1.8/rxode2/R/rudfModelC.R |only rxode2-5.1.8/rxode2/R/rudfModelFind.R |only rxode2-5.1.8/rxode2/R/rudfModelLookup.R |only rxode2-5.1.8/rxode2/R/rudfModelReg.R |only rxode2-5.1.8/rxode2/R/rudfModelScope.R |only rxode2-5.1.8/rxode2/R/rudfui.R | 455 rxode2-5.1.8/rxode2/R/rxEvent.R |only rxode2-5.1.8/rxode2/R/rxEventEmit.R |only rxode2-5.1.8/rxode2/R/rxFormat.R | 22 rxode2-5.1.8/rxode2/R/rxIndLin.R | 21 rxode2-5.1.8/rxode2/R/rxJacobian.R | 164 rxode2-5.1.8/rxode2/R/rxLinCmt.R | 407 rxode2-5.1.8/rxode2/R/rxMemoryEstimate.R | 450 rxode2-5.1.8/rxode2/R/rxOom.R | 627 rxode2-5.1.8/rxode2/R/rxOptExpr.R | 428 rxode2-5.1.8/rxode2/R/rxParams.R | 166 rxode2-5.1.8/rxode2/R/rxPrune.R | 175 rxode2-5.1.8/rxode2/R/rxRaw.R | 102 rxode2-5.1.8/rxode2/R/rxReq.R | 5 rxode2-5.1.8/rxode2/R/rxResidualError.R | 3 rxode2-5.1.8/rxode2/R/rxSerialize.R | 20 rxode2-5.1.8/rxode2/R/rxShiny.R | 57 rxode2-5.1.8/rxode2/R/rxStack.R | 113 rxode2-5.1.8/rxode2/R/rxSymInv.R | 250 rxode2-5.1.8/rxode2/R/rxSyntaxFunctions.R | 2 rxode2-5.1.8/rxode2/R/rxUiGet.R | 443 rxode2-5.1.8/rxode2/R/rxValidate.R | 19 rxode2-5.1.8/rxode2/R/rxode-options.R | 89 rxode2-5.1.8/rxode2/R/rxode2.R | 1001 rxode2-5.1.8/rxode2/R/rxode2_md5.R | 3 rxode2-5.1.8/rxode2/R/rxrandom.R | 148 rxode2-5.1.8/rxode2/R/rxsolve.R | 4008 +- rxode2-5.1.8/rxode2/R/selu.R | 4 rxode2-5.1.8/rxode2/R/softplus.R | 10 rxode2-5.1.8/rxode2/R/splitBolus.R | 143 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rxode2-5.1.8/rxode2/src/init.c | 125 rxode2-5.1.8/rxode2/src/install.libs.R | 8 rxode2-5.1.8/rxode2/src/invCdfMemo.h |only rxode2-5.1.8/rxode2/src/linCmtSensType.h | 2 rxode2-5.1.8/rxode2/src/par_solve.cpp | 496 rxode2-5.1.8/rxode2/src/par_solve.h | 19 rxode2-5.1.8/rxode2/src/parseAssignStr.h | 5 rxode2-5.1.8/rxode2/src/parseDdt.h | 8 rxode2-5.1.8/rxode2/src/parseDfdy.h | 11 rxode2-5.1.8/rxode2/src/parseFuns.h | 216 rxode2-5.1.8/rxode2/src/parseFunsDiff.h | 39 rxode2-5.1.8/rxode2/src/parseFunsRandom.h | 57 rxode2-5.1.8/rxode2/src/parseLogical.h | 36 rxode2-5.1.8/rxode2/src/parseSyntaxErrors.h | 1 rxode2-5.1.8/rxode2/src/parseVars.h | 43 rxode2-5.1.8/rxode2/src/pkTime.h |only rxode2-5.1.8/rxode2/src/print_node.c | 90 rxode2-5.1.8/rxode2/src/print_node.h | 18 rxode2-5.1.8/rxode2/src/priorDensity.cpp | 276 rxode2-5.1.8/rxode2/src/rk4s.cpp | 5 rxode2-5.1.8/rxode2/src/ros4.cpp | 7 rxode2-5.1.8/rxode2/src/rxCse.cpp | 5 rxode2-5.1.8/rxode2/src/rxCseRun.h | 10 rxode2-5.1.8/rxode2/src/rxCseSel.h | 22 rxode2-5.1.8/rxode2/src/rxData.cpp | 122 rxode2-5.1.8/rxode2/src/rxGlobals.h | 2 rxode2-5.1.8/rxode2/src/rxMemoryComponents.cpp | 8 rxode2-5.1.8/rxode2/src/rxSerialize.cpp | 73 rxode2-5.1.8/rxode2/src/rxode2_df.cpp | 77 rxode2-5.1.8/rxode2/src/rxode2lincmtLink.cpp |only rxode2-5.1.8/rxode2/src/rxode2lincmtLink.h |only rxode2-5.1.8/rxode2/src/rxomp.h | 14 rxode2-5.1.8/rxode2/src/rxthreefry.cpp | 201 rxode2-5.1.8/rxode2/src/rxthreefry.h | 1 rxode2-5.1.8/rxode2/src/seBatch.h | 11 rxode2-5.1.8/rxode2/src/seed.cpp | 8 rxode2-5.1.8/rxode2/src/tran.c | 62 rxode2-5.1.8/rxode2/src/tran.g.d_parser.h |19138 ++++++---- rxode2-5.1.8/rxode2/src/tran.h | 16 rxode2-5.1.8/rxode2/src/utilc.cpp | 111 rxode2-5.1.8/rxode2/tests/testthat.R | 4 rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-corpus.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-grid.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden.R | 335 rxode2-5.1.8/rxode2/tests/testthat/helper-etaDistDirect.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etaDistLotri.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-lincmt-grad.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-lincmt-origin.R | 27 rxode2-5.1.8/rxode2/tests/testthat/helper-lotri.R | 3 rxode2-5.1.8/rxode2/tests/testthat/helper-methods.R | 130 rxode2-5.1.8/rxode2/tests/testthat/helper-symengine-fixture.R |only rxode2-5.1.8/rxode2/tests/testthat/nmtest-pktime.rds |only rxode2-5.1.8/rxode2/tests/testthat/test-000-modelVars.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-001-sum.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-abi-subject-stride.R | 95 rxode2-5.1.8/rxode2/tests/testthat/test-activation.R | 306 rxode2-5.1.8/rxode2/tests/testthat/test-adaptive-dosing-arg-vars.R | 128 rxode2-5.1.8/rxode2/tests/testthat/test-adjoint-discrete.R | 1740 rxode2-5.1.8/rxode2/tests/testthat/test-adjoint-sens.R | 583 rxode2-5.1.8/rxode2/tests/testthat/test-alag-first-record-cov.R 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rxode2-5.1.8/rxode2/tests/testthat/test-lhs-ifelse.R | 104 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-lag-symengine.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lhs-lag.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-param.R | 29 rxode2-5.1.8/rxode2/tests/testthat/test-lhs-str.R | 284 rxode2-5.1.8/rxode2/tests/testthat/test-linCmtMicro.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-alag-batch.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-carry-live.R | 81 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-cmt-ref.R | 10 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-delta-memo.R | 135 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-dose-time-sens.R | 98 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-dual.R | 129 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-link.R |only rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-modelvars.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-neg-depot-1275.R | 56 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-origin-limits.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-origin-sens.R | 83 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-partial-mask-ss.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-phi-analytic.R | 115 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-phi-engage.R | 80 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sens-adr-threads.R | 58 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sens-auto.R | 86 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-sensH-1276.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-seq-tail.R | 114 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-solve-sens.R | 43 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-solve.R | 335 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-state-read.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-lincmt-value-memo.R | 149 rxode2-5.1.8/rxode2/tests/testthat/test-llik.R | 256 rxode2-5.1.8/rxode2/tests/testthat/test-locally-constant-se.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-lock.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-logical.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-logit.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-meanProb.R | 111 rxode2-5.1.8/rxode2/tests/testthat/test-memory-growth.R | 57 rxode2-5.1.8/rxode2/tests/testthat/test-mexp-nonmem.R | 735 rxode2-5.1.8/rxode2/tests/testthat/test-missing-evid.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-mix.R | 151 rxode2-5.1.8/rxode2/tests/testthat/test-mlogit.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-model-fun-types.R |only rxode2-5.1.8/rxode2/tests/testthat/test-model-rate.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-modelargs.R | 7 rxode2-5.1.8/rxode2/tests/testthat/test-mtime.R | 61 rxode2-5.1.8/rxode2/tests/testthat/test-mu.R | 824 rxode2-5.1.8/rxode2/tests/testthat/test-mu2.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-multi.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-multisim-shared-event-oob.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-nearpd.R | 61 rxode2-5.1.8/rxode2/tests/testthat/test-nested-sim-iov-cor.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-nesting.R | 49 rxode2-5.1.8/rxode2/tests/testthat/test-nmtest.R | 356 rxode2-5.1.8/rxode2/tests/testthat/test-nodup-keep.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-nonmem-pk-time.R |only rxode2-5.1.8/rxode2/tests/testthat/test-nopred-ui.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-nsim-ind-alloc-412.R | 58 rxode2-5.1.8/rxode2/tests/testthat/test-null-assign.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-occ.R | 485 rxode2-5.1.8/rxode2/tests/testthat/test-odeToLin.R | 278 rxode2-5.1.8/rxode2/tests/testthat/test-omega-chol.R | 68 rxode2-5.1.8/rxode2/tests/testthat/test-omega-varcov.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-omegaCubeConvert.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-omegaRse.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-omp-num-threads.R | 77 rxode2-5.1.8/rxode2/tests/testthat/test-oom.R | 468 rxode2-5.1.8/rxode2/tests/testthat/test-opt-expr.R | 424 rxode2-5.1.8/rxode2/tests/testthat/test-optexpr-cse-c.R | 141 rxode2-5.1.8/rxode2/tests/testthat/test-optexpr-fixture.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-par-dop853.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-par-loader.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-par-solve.R | 189 rxode2-5.1.8/rxode2/tests/testthat/test-param-order.R | 160 rxode2-5.1.8/rxode2/tests/testthat/test-param-statements.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parse-double-sign.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parse-empty-statement.R | 117 rxode2-5.1.8/rxode2/tests/testthat/test-parse-translation-gc.R |only rxode2-5.1.8/rxode2/tests/testthat/test-parsefuns-compile.R | 72 rxode2-5.1.8/rxode2/tests/testthat/test-parsing.R | 251 rxode2-5.1.8/rxode2/tests/testthat/test-pheno.R | 23 rxode2-5.1.8/rxode2/tests/testthat/test-pipeline.R | 49 rxode2-5.1.8/rxode2/tests/testthat/test-piping-equivalence.R |only rxode2-5.1.8/rxode2/tests/testthat/test-piping-ini.R | 181 rxode2-5.1.8/rxode2/tests/testthat/test-piping-reserved-vars.R | 84 rxode2-5.1.8/rxode2/tests/testthat/test-pkg-exported-funs.R | 618 rxode2-5.1.8/rxode2/tests/testthat/test-plogis.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-plot.R | 56 rxode2-5.1.8/rxode2/tests/testthat/test-print.R | 538 rxode2-5.1.8/rxode2/tests/testthat/test-prior-density.R | 691 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-nested.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-nwpri.R | 50 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-spec.R | 66 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-tnpri-general.R | 318 rxode2-5.1.8/rxode2/tests/testthat/test-prior-sim-tnpri.R | 75 rxode2-5.1.8/rxode2/tests/testthat/test-progress.R |only rxode2-5.1.8/rxode2/tests/testthat/test-random.R | 161 rxode2-5.1.8/rxode2/tests/testthat/test-raw.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rbind.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-recompile-model.R | 8 rxode2-5.1.8/rxode2/tests/testthat/test-resample-time-varying.R |only rxode2-5.1.8/rxode2/tests/testthat/test-resample.R | 264 rxode2-5.1.8/rxode2/tests/testthat/test-reserved-names.R |only rxode2-5.1.8/rxode2/tests/testthat/test-reset.R | 16 rxode2-5.1.8/rxode2/tests/testthat/test-rhs.R | 31 rxode2-5.1.8/rxode2/tests/testthat/test-rk-decay.R | 120 rxode2-5.1.8/rxode2/tests/testthat/test-rk-order.R | 152 rxode2-5.1.8/rxode2/tests/testthat/test-rk4.R | 25 rxode2-5.1.8/rxode2/tests/testthat/test-rx2api-parallel-error.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rxFix.R | 130 rxode2-5.1.8/rxode2/tests/testthat/test-rxMemoryEstimate.R | 256 rxode2-5.1.8/rxode2/tests/testthat/test-rxRmvn.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-rxStack-factor.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-rxState.R |only rxode2-5.1.8/rxode2/tests/testthat/test-rxSumProd.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-rxUiDeparse.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-rxflag.R | 10 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-007.R | 116 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-050.R | 24 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-054.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-056.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-067.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-1211.R | 28 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-1229.R | 26 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-160.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-163.R | 41 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-169.R | 29 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-178.R | 8 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-213.R | 88 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-299.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-349.R | 42 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-375.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-393.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-410.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-430.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-431.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-445.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-449.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-450.R | 127 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-468.R | 134 rxode2-5.1.8/rxode2/tests/testthat/test-rxode-issue-982.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-rxpre-cache-key.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-rxs-function-cache.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-rxs.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-rxsolve-ui-dispatch.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-rxui-ctl.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-s3-delayed-register.R | 37 rxode2-5.1.8/rxode2/tests/testthat/test-safeZero.R | 118 rxode2-5.1.8/rxode2/tests/testthat/test-scale.R | 136 rxode2-5.1.8/rxode2/tests/testthat/test-seed-threads.R |only rxode2-5.1.8/rxode2/tests/testthat/test-sens3.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-seq.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-serialize.R | 168 rxode2-5.1.8/rxode2/tests/testthat/test-sigdig-tol.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-sigma-hom-et-1341.R | 38 rxode2-5.1.8/rxode2/tests/testthat/test-sigma-one-obs-1364.R |only rxode2-5.1.8/rxode2/tests/testthat/test-sim-err-670.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-sim-zeros.R | 67 rxode2-5.1.8/rxode2/tests/testthat/test-solComp.R | 4225 +- rxode2-5.1.8/rxode2/tests/testthat/test-solve-warn-id.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-solver-basic.R | 57 rxode2-5.1.8/rxode2/tests/testthat/test-sortids-throttle.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-ss-extra-dose-duration.R | 20 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-dur.R | 115 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-f.R | 100 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-lag.R | 30 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-rate.R | 117 rxode2-5.1.8/rxode2/tests/testthat/test-state-dep-sort.R | 9 rxode2-5.1.8/rxode2/tests/testthat/test-statePropDf.R | 169 rxode2-5.1.8/rxode2/tests/testthat/test-steady-state.R | 89 rxode2-5.1.8/rxode2/tests/testthat/test-sticky-vars.R | 32 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-constants-downstream.R | 87 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-constants.R | 14 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-rxq-string.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-second-derivative.R |only rxode2-5.1.8/rxode2/tests/testthat/test-symengine-simplify.R | 33 rxode2-5.1.8/rxode2/tests/testthat/test-symengine-translate-fixture-toSE.R |only rxode2-5.1.8/rxode2/tests/testthat/test-symengine-translate-fixture.R | 141 rxode2-5.1.8/rxode2/tests/testthat/test-symmetric.R | 43 rxode2-5.1.8/rxode2/tests/testthat/test-symplectic-solvers.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-tad-infusion-after-bolus.R | 51 rxode2-5.1.8/rxode2/tests/testthat/test-tad.R | 1637 rxode2-5.1.8/rxode2/tests/testthat/test-theta-eta.R | 2 rxode2-5.1.8/rxode2/tests/testthat/test-tied-modeled-rate-dur.R | 45 rxode2-5.1.8/rxode2/tests/testthat/test-tlast-rxS.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-tolFactor.R | 21 rxode2-5.1.8/rxode2/tests/testthat/test-transit.R | 13 rxode2-5.1.8/rxode2/tests/testthat/test-tvcov-modeled-dur.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model-c.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model-scope.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-model.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf-search-list.R |only rxode2-5.1.8/rxode2/tests/testthat/test-udf.R | 545 rxode2-5.1.8/rxode2/tests/testthat/test-ui-assembled.R | 189 rxode2-5.1.8/rxode2/tests/testthat/test-ui-assert.R | 337 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rxode2-5.1.8/rxode2/tests/testthat/test-ui-model.R | 50 rxode2-5.1.8/rxode2/tests/testthat/test-ui-modelExtract.R | 94 rxode2-5.1.8/rxode2/tests/testthat/test-ui-modelName.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-ui-multiple-endpoint.R | 81 rxode2-5.1.8/rxode2/tests/testthat/test-ui-mv.R | 53 rxode2-5.1.8/rxode2/tests/testthat/test-ui-piping-single-endpoint.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-piping.R | 1550 rxode2-5.1.8/rxode2/tests/testthat/test-ui-pred-err.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-promote.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-props.R | 128 rxode2-5.1.8/rxode2/tests/testthat/test-ui-rename.R | 67 rxode2-5.1.8/rxode2/tests/testthat/test-ui-simulation.R | 233 rxode2-5.1.8/rxode2/tests/testthat/test-ui-single-theta.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-ui-solve.R | 3 rxode2-5.1.8/rxode2/tests/testthat/test-ui.R | 595 rxode2-5.1.8/rxode2/tests/testthat/test-unload.R |only rxode2-5.1.8/rxode2/tests/testthat/test-yeojohnson-derivative.R | 11 rxode2-5.1.8/rxode2/tests/testthat/test-zzzz-plot.R | 33 rxode2-5.1.8/rxode2/tests/testthat/test-zzzz-rxUse.R | 10 629 files changed, 65681 insertions(+), 36415 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level". Messages are signalled as classed R conditions, so that calling code can decide how serious a situation is, rather than the function which detects it having to be told in advance.
Author: Jon Clayden [aut, cre]
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.3.1 dated 2025-03-29 and 2.0.0 dated 2026-10-13
reportr-1.3.1/reportr/R/reportr.R |only reportr-1.3.1/reportr/man/reportr.Rd |only reportr-2.0.0/reportr/DESCRIPTION | 17 reportr-2.0.0/reportr/MD5 | 32 + reportr-2.0.0/reportr/NAMESPACE | 10 reportr-2.0.0/reportr/NEWS | 95 ++++ reportr-2.0.0/reportr/R/00_constants.R | 10 reportr-2.0.0/reportr/R/conditions.R |only reportr-2.0.0/reportr/R/fallback.R |only reportr-2.0.0/reportr/R/handlers.R |only reportr-2.0.0/reportr/R/render.R |only reportr-2.0.0/reportr/R/report.R |only reportr-2.0.0/reportr/R/reportr-package.R |only reportr-2.0.0/reportr/README.md | 316 +++++++++++---- reportr-2.0.0/reportr/inst/tinytest/test-10-ask.R | 45 +- reportr-2.0.0/reportr/inst/tinytest/test-20-conditions.R |only reportr-2.0.0/reportr/inst/tinytest/test-25-fallback.R |only reportr-2.0.0/reportr/inst/tinytest/test-30-reportAs.R |only reportr-2.0.0/reportr/inst/tinytest/test-35-handlers.R |only reportr-2.0.0/reportr/inst/tinytest/test-40-targets.R |only reportr-2.0.0/reportr/man/fallback.Rd |only reportr-2.0.0/reportr/man/handlers.Rd |only reportr-2.0.0/reportr/man/report.Rd |only reportr-2.0.0/reportr/man/reportr-package.Rd |only reportr-2.0.0/reportr/man/reportrCondition.Rd |only reportr-2.0.0/reportr/man/setOutputLevel.Rd |only reportr-2.0.0/reportr/man/targets.Rd |only 27 files changed, 429 insertions(+), 96 deletions(-)
Title: Data Envelopment Analysis for Pollution-Generating Technologies
Description: Nonparametric efficiency analysis for pollution-generating
technologies under the materials-balance principle. Implements the
weak-G-disposability technology of Hampf and Rodseth (2015)
<doi:10.1016/j.eneco.2015.04.001>, scored by the minimal-emission
programme of Rodseth (2025) <doi:10.1007/s11123-025-00768-0> with
its directional representation and five-component decomposition,
the by-production intersection
technology of Murty, Russell and Levkoff (2012)
<doi:10.1016/j.jeem.2012.02.005>, the materials-balance cost model of
Coelli, Lauwers and Van Huylenbroeck (2007)
<doi:10.1007/s11123-007-0052-8> and a weak-disposability reference
model, with a pre-estimation audit of every materials-balance
account, metafrontier decompositions, bad-output shadow prices,
marginal abatement cost curves, a cross-axiom comparison harness, a
global Malmquist-Luenberger productivity index and subsampling
sensitivity intervals. Estimators are solved with 'lpSolveAPI'.
Author: Erik Enstad [aut, cre]
Maintainer: Erik Enstad <erik.enstad@nhh.no>
Diff between pgt versions 0.7.0 dated 2026-09-22 and 0.7.1 dated 2026-10-13
DESCRIPTION | 16 +- MD5 | 84 +++++----- NEWS.md | 155 +++++++++++++++++++ R/boot.R | 29 ++- R/compare_models.R | 31 +++ R/data.R | 17 +- R/decompose.R | 24 ++- R/lp_solvers.R | 251 +++++++++++++++++++++++++------ R/ml_index.R | 52 ++++-- R/pgt.R | 121 ++++++++++----- README.md | 14 + inst/doc/comparing-axioms.Rmd | 16 +- inst/doc/comparing-axioms.html | 26 +-- inst/doc/introduction.Rmd | 19 +- inst/doc/introduction.html | 63 ++++--- inst/doc/models.Rmd | 83 +++++++--- inst/doc/models.html | 100 +++++++++--- inst/doc/productivity.R | 13 + inst/doc/productivity.Rmd | 87 +++++++---- inst/doc/productivity.html | 142 ++++++++++++------ inst/doc/replication.R | 35 ++-- inst/doc/replication.Rmd | 108 +++++++------ inst/doc/replication.html | 268 ++++++++++++++++++---------------- inst/simulations/coverage-reps.csv |only inst/simulations/coverage-results.csv | 16 +- inst/simulations/coverage.R | 156 ++++++++++++++----- man/boot_pgt.Rd | 29 ++- man/compare_models.Rd | 9 + man/pgt.Rd | 112 +++++++++----- man/pgt_decompose.Rd | 24 ++- man/pgt_ml.Rd | 45 +++-- man/pigfarms.Rd | 13 + man/uscoal.Rd | 4 tests/testthat/test-byprod.R | 6 tests/testthat/test-compare.R | 17 ++ tests/testthat/test-fdmo.R | 46 +++++ tests/testthat/test-pigfarms.R | 59 +++++-- tests/testthat/test-scaling.R |only tests/testthat/test-wgd.R | 15 + vignettes/comparing-axioms.Rmd | 16 +- vignettes/introduction.Rmd | 19 +- vignettes/models.Rmd | 83 +++++++--- vignettes/productivity.Rmd | 87 +++++++---- vignettes/replication.Rmd | 108 +++++++------ 44 files changed, 1823 insertions(+), 795 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.2 dated 2026-08-31 and 1.1.0 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- src/algebra.cpp | 3 +++ src/identification.cpp | 16 ++++++++++++---- src/identification.h | 2 ++ src/random.cpp | 16 +++++++++++++--- src/random.h | 1 + tests/testthat/test-one-option.R | 2 +- 8 files changed, 42 insertions(+), 18 deletions(-)
Title: Inequality Measures for Weighted Data
Description: Computes inequality measures of a given variable taking into account weights. Suitable for ratio, interval and ordered scale. Includes measures developed by Gini, Theil, Leti, Palma ratio, 20:20 ratio, Allison and Foster, Jenkins, Cowell and Flechaire, Abul Naga and Yalcin, Apouey, Blair and Lacy. Bootstrap provides distribution of inequality measures enabling significance tests.
Author: Sebastian Wojcik [aut, cre] ,
Agnieszka Giemza [aut],
Jaroslaw Napora [aut]
Maintainer: Sebastian Wojcik <S.Wojcik@stat.gov.pl>
Diff between wINEQ versions 1.2.2 dated 2026-04-23 and 1.2.3 dated 2026-10-13
DESCRIPTION | 10 MD5 | 47 +-- NAMESPACE | 7 NEWS.md | 237 ++++++++------- R/inequalityMeasure.R | 660 ++++++++++++++++++++++++++++++++++---------- R/inequalityMeasureBoot.R | 574 ++++++++++++++++++++------------------ data/Tourism.rda |binary man/Abul_Naga_and_Yalcin.Rd | 17 - man/Allison_and_Foster.Rd | 21 - man/Apouey.Rd | 13 man/Atkinson.Rd | 8 man/Blair_Lacy.Rd | 17 - man/Bonferroni.Rd |only man/Gini.Rd | 6 man/Hoover.Rd | 1 man/Jenkins.Rd | 1 man/Kakwani.Rd |only man/Leti.Rd | 14 man/LowerSum.Rd | 1 man/Rosenbluth.Rd |only man/SST.Rd |only man/Theil_T.Rd | 2 man/Wolfson.Rd |only man/Zenga.Rd |only man/figures |only man/ineq_weighted.Rd | 20 + man/ineq_weighted_boot.Rd | 18 + man/medianf.Rd | 2 28 files changed, 1067 insertions(+), 609 deletions(-)
Title: Time Series Forecasting Using Nearest Neighbors
Description: Allows forecasting time series using nearest neighbors regression
Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
Rivera (2019) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is univariate and autoregressive, that is, it is only based
on the observations of the time series. The nearest neighbors used in a
prediction can be consulted and plotted.
Author: Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfknn versions 0.6.0 dated 2023-12-20 and 0.7.1 dated 2026-10-13
DESCRIPTION | 14 ++++++------ MD5 | 28 ++++++++++++------------- NEWS.md | 5 +++- R/forecasting.R | 37 +++++++++++++++++----------------- R/knn.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tsfknn.html | 26 +++++++++++------------ man/knn_examples.Rd | 17 +++++++-------- man/knn_forecasting.Rd | 2 - man/n_training_examples.Rd | 4 +-- man/nearest_neighbors.Rd | 4 +-- man/tsfknn-package.Rd | 7 +++++- src/code.cpp | 6 ++--- tests/testthat/test_knn_forecasting.R | 14 ++++++++++++ 15 files changed, 93 insertions(+), 72 deletions(-)
Title: Estimating Trend, Velocity, and Acceleration from Sea Level
Records
Description: Provides tools for analysing annual average ocean water level time series,
estimating mean sea level trends, velocities, and accelerations using Singular
Spectrum Analysis (SSA). The detailed methodology for resolving mean sea level
with improved temporal resolution follows Watson (2018)
"Improved Techniques to Estimate Mean Sea Level, Velocity and Acceleration from
Long Ocean Water Level Time Series to Augment Sea Level (and Climate Change)
Research" <https://unsworks.unsw.edu.au/entities/publication/5e835c87-aa0a-4457-807e-29d354e91d45>.
Additional methodological developments and applications are described in Watson (2020)
"Status of Mean Sea Level Rise around the USA" <doi:10.3390/geohazards2020005>
and Watson and Lim (2020) "An Update on the Status of Mean Sea Level Rise around
the Korean Peninsula" <doi:10.3390/atmos11111153>. Includes multiple gap-filling
methods for incomplete records, diagnostic tools for inspecting SSA components,
and plotting functions for g [...truncated...]
Author: Phil Watson [aut, cre]
Maintainer: Phil Watson <philwatson.slr@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2019-08-07
Diff between TrendSLR versions 1.0 dated 2019-08-07 and 2.0.0 dated 2026-10-13
DESCRIPTION | 55 +++++++++++++---------- MD5 | 40 ++++++++--------- NAMESPACE | 1 R/balt-data.R | 4 - R/check.decomp.R | 42 +++++++++-------- R/custom.trend.R | 34 ++++++-------- R/msl-name.R | 4 + R/msl.fileplot.R | 29 ++++++------ R/msl.screenplot.R | 16 ++++-- R/msltrend.R | 40 ++++++++--------- man/Balt.Rd | 10 ++-- man/TrendSLR.Rd | 104 +++++++++++++++++++++++--------------------- man/check.decomp.Rd | 93 ++++++++++++++++++++++----------------- man/custom.trend.Rd | 115 ++++++++++++++++++++++++++----------------------- man/gap.fillview.Rd | 37 +++++++-------- man/msl.fileplot.Rd | 35 +++++++++----- man/msl.screenplot.Rd | 23 +++++---- man/msl.trend.Rd | 117 ++++++++++++++++++++++++++------------------------ man/s.Rd | 4 + man/summary.Rd | 5 ++ man/t.Rd | 4 + 21 files changed, 445 insertions(+), 367 deletions(-)
Title: ROC-Based Methods for Comparing Survival Distributions with
Right, Left, and Doubly Censored Data
Description: Implements nonparametric and semiparametric methods for comparing two survival distributions under non-proportional hazards (non-PH) with right, left, or doubly censored data. The methods are based on the Receiver Operating Characteristic (ROC) curve length and its kernel-based estimate (Bantis et al. (2021) <doi:10.1002/sim.8869>) and the overlap coefficient (OVL) and its kernel-based estimate (Schmid and Schmidt (2006) <doi:10.1016/j.csda.2005.01.014>), as well as a new joint inference approach involving both the kernel-based ROC length and the kernel-based OVL. These methods do not require prior knowledge of the underlying non-PH pattern. The methods also accommodate the "last is censored" phenomenon for right-censored data by using flexible parametric approaches only for the portion of the tail of the distribution that corresponds to time values beyond the last observed event (see also Bantis et al. (2017) <doi:10.1002/sim.7394>). The analogous "first is censored" [...truncated...]
Author: Mohammod Mahmudur Rahman [aut, cre],
Leonidas Bantis [aut]
Maintainer: Mohammod Mahmudur Rahman <mahmudur.asif13@gmail.com>
Diff between ROCsurvcomp versions 0.1.2 dated 2026-05-11 and 0.1.3 dated 2026-10-13
DESCRIPTION | 12 ++--- MD5 | 12 ++--- NAMESPACE | 50 ++++++++++++---------- NEWS.md | 6 ++ inst/doc/ROCsurvcomp.Rmd | 2 inst/doc/ROCsurvcomp.html | 101 ++++++++++++++++++++++------------------------ vignettes/ROCsurvcomp.Rmd | 2 7 files changed, 97 insertions(+), 88 deletions(-)
Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>).
ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information
about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys.
More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>.
The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] ,
Luana Francesconi [aut],
Alice Musina [aut],
Luca Di Nuzzo [aut],
Gabriele Gheza [aut],
Chiara Pistocchi [aut],
Juri Nascimbene [aut],
Pier Luigi Nimis [aut],
Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Diff between ritalic versions 0.13.0 dated 2026-10-12 and 0.13.1 dated 2026-10-13
DESCRIPTION | 6 +-- MD5 | 4 +- tests/testthat/test_api_utils.R | 66 ++++++++++++++++++++++++---------------- 3 files changed, 45 insertions(+), 31 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.5 dated 2026-10-13 and 1.0.6 dated 2026-10-13
DESCRIPTION | 6 ++-- MD5 | 6 ++-- R/drw.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++------- man/drw.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++----- 4 files changed, 127 insertions(+), 21 deletions(-)
Title: Restricted Bridge Estimation
Description: Implements bridge regression with linear coefficient restrictions
using the local quadratic approximation described by Yuzbasi, Arashi and
Akdeniz (2021) <doi:10.1007/s00500-021-05763-9>. Provides coefficient paths,
cross-validation, prediction and coefficient extraction for restricted and
unrestricted linear models.
Author: Bahadir Yuzbasi [aut, cre],
Mohammad Arashi [aut],
Fikri Akdeniz [aut],
Jerome Friedman [ctb] ,
Trevor Hastie [ctb] ,
Robert Tibshirani [ctb]
Maintainer: Bahadir Yuzbasi <b.yzb@hotmail.com>
Diff between rbridge versions 1.0.3 dated 2026-10-11 and 1.0.4 dated 2026-10-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 11 ++++++++++- README.md | 18 ++++++++++++------ inst/doc/getting-started.html | 2 +- src/Main_functions.cpp | 1 - src/Makevars | 2 ++ src/Makevars.win | 2 ++ 8 files changed, 38 insertions(+), 20 deletions(-)
Title: Multilevel Unanchored Meta-Regression for Indirect Treatment
Comparisons
Description: Bayesian multilevel unanchored meta-regression (ML-UMR) for
indirect treatment comparisons using individual patient data (IPD) and
aggregate data (AgD). Implements shared prognostic factor assumption
(SPFA) and relaxed SPFA models for binary, continuous, count, and
time-to-event (survival) outcomes via 'Stan', including parametric and
flexible M-spline survival baselines. Also provides a one-arm simulated
treatment comparison (STC) via comparator-population G-computation and
naive unadjusted benchmarks. ML-UMR is an adaptation of the ML-NMR
methodology (Phillippo et al. 2020,
<doi:10.1111/rssa.12579>) implemented in the 'multinma' package
(GPL-3) to the unanchored two-trial case. The public API uses familiar
names for data setup, integration and effect summaries, but ML-NMR and
ML-UMR specifications and fitted objects are not interchangeable because
their evidence structures and models differ.
Author: Ahmad Sofi-Mahmudi [aut, cre] ,
Conor Chandler [aut]
Maintainer: Ahmad Sofi-Mahmudi <a.sofimahmudi@gmail.com>
Diff between mlumr versions 0.1.0 dated 2026-05-20 and 0.2.0 dated 2026-10-13
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mlumr-0.1.0/mlumr/man/dot-bound_unit_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-bounded_wald_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-check_required_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstan_available.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_cache_root.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_compile_dir.Rd |only mlumr-0.1.0/mlumr/man/dot-comparison_names.Rd |only mlumr-0.1.0/mlumr/man/dot-compute_mean_lp.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_effect_choices.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_eta.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_profiles.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_count.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_value.Rd |only mlumr-0.1.0/mlumr/man/dot-drop_missing_rows.Rd |only mlumr-0.1.0/mlumr/man/dot-ensure_positive_definite_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-finite_numeric_values.Rd |only mlumr-0.1.0/mlumr/man/dot-generate_copula_uniforms.Rd 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mlumr-0.1.0/mlumr/man/dot-require_draw_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-rescale_prior_beta.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_integration_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_mlumr_engine.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_broadcast_label.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_family_label.Rd |only mlumr-0.1.0/mlumr/man/dot-safe_positive_ratio.Rd |only mlumr-0.1.0/mlumr/man/dot-sqrt_variance.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_agd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_ipd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_agd_mean_newdata.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_comparator_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_index_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_comparator_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_formula.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_glm_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_model_matrix.Rd 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mlumr-0.2.0/mlumr/vignettes/data-preparation.Rmd | 440 - mlumr-0.2.0/mlumr/vignettes/fitting-and-diagnostics.html.asis |only mlumr-0.2.0/mlumr/vignettes/introduction.Rmd | 231 - mlumr-0.2.0/mlumr/vignettes/subgroup-identification.html.asis |only mlumr-0.2.0/mlumr/vignettes/survival-outcomes.html.asis |only 361 files changed, 19714 insertions(+), 8372 deletions(-)
Title: Hierarchical Risk Clustering Portfolio Allocation Strategies
Description: Machine learning hierarchical risk clustering portfolio allocation strategies.
The implemented methods are:
Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
Hierarchical clustering-based asset allocation (Raffinot, 2017)
<DOI: 10.3905/jpm.2018.44.2.089>.
Hierarchical equal risk contribution portfolio (Raffinot, 2018)
<DOI: 10.2139/ssrn.3237540>.
A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
<https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Hierarchical Risk Budgeting (Koumou, 2024) <DOI: 10.3905/jfds.2024.1.156>.
Author: Carlos Trucios [aut, cre] ,
Moon Jun Kwon [aut],
Sao Paulo Research Foundation , grants 2022/09122-0,
2025/06131-7 and 2025/08502-2 [fnd],
Programa de Incentivo a Novos Docentes da UNICAMP , grant 2525/23
[fnd]
Maintainer: Carlos Trucios <ctrucios@unicamp.br>
Diff between HierPortfolios versions 1.0.2 dated 2025-09-12 and 1.1.0 dated 2026-10-13
DESCRIPTION | 16 +++++++++------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + R/DHRP_Portfolio.R | 4 ++-- R/HCAA_Portfolio.R | 4 ++-- R/HERC_Portfolio.R | 18 +++++++----------- R/HRB_Portfolio.R |only R/HRP_Portfolio.R | 4 ++-- man/DHRP_Portfolio.Rd | 4 ++-- man/HCAA_Portfolio.Rd | 4 ++-- man/HERC_Portfolio.Rd | 4 ++-- man/HRB_Portfolio.Rd |only man/HRP_Portfolio.Rd | 4 ++-- 13 files changed, 43 insertions(+), 42 deletions(-)
More information about HierPortfolios at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue (202 [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.5 dated 2026-09-25 and 1.5.6 dated 2026-10-13
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS | 4 ++++ R/scraping_games_acb.R | 2 +- inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- inst/doc/BAwiR_sc.html | 4 ++-- 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.9 dated 2026-08-28 and 0.5.0 dated 2026-10-13
DESCRIPTION | 11 MD5 | 34 - NAMESPACE | 10 NEWS.md | 390 ++++++------ R/cms_download_native.R | 9 R/cms_download_subset.r | 983 +++++++++++++++---------------- R/import.r | 2 README.md | 6 build/vignette.rds |binary inst/doc/blosc.html | 5 inst/doc/glossary.html | 4 inst/doc/product-info.html | 7 inst/doc/proxy.html | 11 inst/doc/translate.html | 7 man/cms_native_s3.Rd | 1 man/figures/README-download-subset-1.png |binary tests/testthat/test_login.r | 2 tests/testthat/test_subset.r | 442 +++++++------ 18 files changed, 981 insertions(+), 943 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Citations are:
* Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
* Luis F.S. Castro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and Timothy Charles Bates (2026). umx version 4.5: Extending Twin and Path-Based SEM in R with CLPM, MR-DoC, Definition Variables, Onyx Integration, and Censored Distributions. Twin Research and Human Genetics, 1-6. <doi:10.1017/thg.2026.10056>.
Author: Timothy C. Bates [aut, cre] ,
Luis De Araujo [ctb],
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.80.0 dated 2026-10-11 and 4.80.1 dated 2026-10-13
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Title: Post-Linkage Data Analysis
Description: Provides a suite of statistical tools for post-linkage data analysis (PLDA), designed to account for record linkage errors in downstream modeling. The package implements a familiar, formula-based regression interface that adjusts for linkage uncertainty, accommodating workflows where direct access to unlinked primary files is restricted. It consolidates diverse adjustment methodologies, all of which support generalized linear models (linear, logistic, Poisson, and Gamma). These methodologies include weighting approaches (Chambers (2009) <https://hdl.handle.net/10779/uow.27788247>; Chambers et al. (2023) <doi:10.1002/wics.1596>), mixture modeling (Slawski et al. (2025) <doi:10.1093/jrsssa/qnae083>), and Bayesian mixture modeling (Gutman et al. (2016) <doi:10.1002/sim.6586>). For time-to-event data, both the weighting (Vo et al. (2024) <doi:10.1002/sim.9960>) and mixture modeling approaches accommodate Cox proportional hazards models, while the Bayesian appr [...truncated...]
Author: Priyanjali Bukke [aut, cre],
Gauri Kamat [aut],
Jiahao Cui [aut],
Roee Gutman [aut],
Martin Slawski [aut],
Zhenbang Wang [ctb],
Brady T. West [ctb],
Emanuel Ben-David [ctb],
Guoqing Diao [ctb]
Maintainer: Priyanjali Bukke <postlink.group@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2026-09-04
Diff between postlink versions 0.1.1 dated 2026-09-04 and 0.1.2 dated 2026-10-13
DESCRIPTION | 12 - MD5 | 110 ++++++------ NEWS.md | 13 + R/mixture_coxph.R | 33 ++- R/mixture_glm.R | 120 ++++++------- README.md | 16 + configure.win | 3 inst/stan/glmMixBayes_binomial.stan | 4 inst/stan/glmMixBayes_gamma.stan | 2 inst/stan/glmMixBayes_gaussian.stan | 2 inst/stan/glmMixBayes_poisson.stan | 4 inst/stan/survMixBayes_gamma.stan | 4 inst/stan/survMixBayes_weibull.stan | 4 man/adjELE.Rd | 180 ++++++++++---------- man/adjMixture.Rd | 182 ++++++++++---------- man/brfss.Rd | 106 +++++------ man/confint.coxphELE.Rd | 124 ++++++------- man/confint.coxphMixture.Rd | 142 +++++++-------- man/confint.glmELE.Rd | 82 ++++----- man/confint.glmMixture.Rd | 110 ++++++------ man/coxphELE.Rd | 192 ++++++++++----------- man/coxphMixture.Rd | 242 +++++++++++++------------- man/ctableMixture.Rd | 204 +++++++++++----------- man/glmELE.Rd | 166 +++++++++--------- man/glmMixture.Rd | 186 ++++++++++---------- man/predict.coxphELE.Rd | 140 +++++++-------- man/predict.coxphMixture.Rd | 208 +++++++++++------------ man/predict.glmELE.Rd | 132 +++++++------- man/predict.glmMixture.Rd | 160 ++++++++--------- man/print.adjELE.Rd | 78 ++++---- man/print.adjMixture.Rd | 88 ++++----- man/print.coxphELE.Rd | 116 ++++++------ man/print.coxphMixture.Rd | 122 ++++++------- man/print.glmELE.Rd | 74 ++++---- man/print.glmMixture.Rd | 92 +++++----- man/summary.coxphELE.Rd | 132 +++++++------- man/summary.coxphMixture.Rd | 148 ++++++++-------- man/summary.glmELE.Rd | 80 ++++---- man/summary.glmMixture.Rd | 108 ++++++------ man/vcov.coxphELE.Rd | 114 ++++++------ man/vcov.coxphMixture.Rd | 142 +++++++-------- man/vcov.glmELE.Rd | 74 ++++---- man/vcov.glmMixture.Rd | 94 +++++----- src/Makevars.win | 2 src/stanExports_glmMixBayes_binomial.cc | 34 +-- src/stanExports_glmMixBayes_binomial.h | 181 ++++++++++++++------ src/stanExports_glmMixBayes_gamma.cc | 34 +-- src/stanExports_glmMixBayes_gamma.h | 233 ++++++++++++++++++------- src/stanExports_glmMixBayes_gaussian.cc | 34 +-- src/stanExports_glmMixBayes_gaussian.h | 220 +++++++++++++++++------- src/stanExports_glmMixBayes_poisson.cc | 34 +-- src/stanExports_glmMixBayes_poisson.h | 181 ++++++++++++++------ src/stanExports_survMixBayes_gamma.cc | 34 +-- src/stanExports_survMixBayes_gamma.h | 273 +++++++++++++++++++++--------- src/stanExports_survMixBayes_weibull.cc | 34 +-- src/stanExports_survMixBayes_weibull.h | 287 +++++++++++++++++++++++--------- 56 files changed, 3283 insertions(+), 2643 deletions(-)
Title: One-Way Statistical Analyses
Description: Performs one-way tests of assumptions (normality and homoscedasticity),
analysis of variance, robust and nonparametric alternatives, multiple comparison
procedures, effect size estimators, confidence intervals, and descriptive summaries.
Functions are designed with a consistent interface to support reproducible and
user-friendly statistical workflows. For more details see
Howell (2010, ISBN:978-0-495-59784-1),
Zar (2014, ISBN:978-0-13-100846-5),
Hollander et al. (2014, ISBN:978-0-470-38737-5),
Montgomery (2017, ISBN:978-1-119-11347-8),
Lakens (2013) <doi:10.3389/fpsyg.2013.00863>, and
Piepho (2004) <doi:10.1198/1061860043515>.
Author: Joon-Keat Lai [aut, cre, cph]
Maintainer: Joon-Keat Lai <p10911004@gmail.com>
Diff between oneway versions 0.0.2 dated 2026-09-15 and 0.0.3 dated 2026-10-13
DESCRIPTION | 26 +++++++++--------- MD5 | 53 +++++++++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 16 +++++++++-- R/Dunn_test.R | 2 - R/Games_Howell_test.R | 4 +- R/REGWQ_test.R | 20 ++++++------- R/Scheffe_test.R |only R/Tukey_HSD_test.R | 16 ++++------- R/Tukey_Kramer_test.R | 4 +- R/anova.R | 34 +++++++++++------------ R/compact_letter_display.R | 2 - R/pairwise_comparison.R | 4 +- R/utils.R | 2 - README.md | 10 ++++++ build |only data/O_O_O.rda |binary inst |only man/Kruskal_Wallis_test.Rd | 8 ++++- man/REGWQ_test.Rd | 16 ++++------- man/Scheffe_test.Rd |only man/Tukey_HSD_test.Rd | 12 +++----- man/oneway_anova.Rd | 2 - man/oneway_art.Rd | 2 - man/pairwise_comparison.Rd | 2 - man/pairwise_contrasts.Rd |only man/simulated_data.Rd | 2 - tests/testthat/test-REGWQ_test.R | 9 ++++-- tests/testthat/test-Scheffe_test.R |only vignettes |only 30 files changed, 143 insertions(+), 105 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.2-6 dated 2026-03-06 and 1.2-7 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Bernstein.R | 40 ++++++++++++++++++++-------------------- R/formula.R | 6 +++--- R/legendre.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ tests/bugfixes.R | 12 ++++++++++++ 9 files changed, 56 insertions(+), 38 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.4 dated 2026-08-20 and 1.0.5 dated 2026-10-13
DESCRIPTION | 8 - MD5 | 6 R/drw.R | 369 ++++++++++++++++++++++++++++++++++++++++++++++-------------- man/drw.Rd | 36 +++-- 4 files changed, 313 insertions(+), 106 deletions(-)
Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.17.4. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
awPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot [aut],
Paul Brooks [aut, cre],
Andrea Visentin [aut],
Young Woong Park [aut],
and Yi-Hui Zhou [aut]
Maintainer: Paul Brooks <jpbrooks@ou.edu>
Diff between pcaL1 versions 1.5.9 dated 2025-05-03 and 1.5.10 dated 2026-10-13
ChangeLog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS | 14 ++++++++++++++ configure | 18 +++++++++--------- configure.ac | 2 +- man/pcaL1-package.Rd | 8 ++++---- src/sparsel1pca.c | 2 +- 8 files changed, 48 insertions(+), 29 deletions(-)
Title: Multipurpose Aids for R Kit
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.3 dated 2025-04-22 and 0.9.0 dated 2026-10-13
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Title: Implement Fleming-Viot-Dependent Dirichlet Processes
Description: A Bayesian Nonparametric model for the study of time-evolving frequencies, which has become renowned in the study of population genetics.
The model consists of a Hidden Markov Model (HMM) in which the latent signal is a distribution-valued stochastic process that takes the form of a finite mixture of Dirichlet Processes, indexed by vectors that count how many times each value is observed in the population.
The package implements methodologies presented in Ascolani, Lijoi and Ruggiero (2021) <doi:10.1214/20-BA1206> and Ascolani, Lijoi and Ruggiero (2023) <doi:10.3150/22-BEJ1504> that make it possible to study the process at the time of data collection or to predict its evolution in future or in the past.
The package itself is described in Ascolani, Damato and Ruggiero (2024) <doi:10.1089/cmb.2024.0600>.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between FVDDPpkg versions 0.1.2 dated 2024-07-09 and 0.1.3 dated 2026-10-13
DESCRIPTION | 11 - MD5 | 13 - README.md | 58 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/FVDDPpkg.html | 489 +++++++++++++++++++++++++------------------------ src/C++FVDDP.cpp | 2 8 files changed, 290 insertions(+), 283 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.5 dated 2020-07-17 and 0.3.6 dated 2026-10-13
ChangeLog | 4 DESCRIPTION | 11 LICENSE | 2 MD5 | 54 - NAMESPACE | 6 NEWS.md | 4 R/configr.R | 1 R/configtype.R | 8 R/parse.R | 16 R/read.R | 14 R/utils.R | 2 README.md | 69 -- build/vignette.rds |binary inst/doc/configr.R | 22 inst/doc/configr.Rmd | 2 inst/doc/configr.html | 1567 ++++++++++++++++++++++++------------------------ inst/doc/filetypes.R | 2 inst/doc/filetypes.Rmd | 2 inst/doc/filetypes.html | 572 +++++++++-------- man/configr.Rd | 1 man/is.ini.file.Rd | 4 man/is.json.file.Rd | 4 man/is.toml.file.Rd | 4 man/is.yaml.file.Rd | 4 man/parse.extra.Rd | 16 man/read.config.Rd | 14 vignettes/configr.Rmd | 2 vignettes/filetypes.Rmd | 2 28 files changed, 1228 insertions(+), 1181 deletions(-)