Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon realms (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package accompanies the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 0.3.0 dated 2024-10-21 and 0.4.0 dated 2024-10-29
rice |only 1 file changed
Title: Common Computational Operations Working with RefSeq Entries
(GenBank)
Description: Fetches NCBI data (RefSeq <https://www.ncbi.nlm.nih.gov/refseq/> database) and provides an environment to
extract information at the level of gene, mRNA or protein accessions.
Author: Jose V. Die [aut, cre] ,
Lluis Revilla Sancho [ctb]
Maintainer: Jose V. Die <jose.die@uco.es>
Diff between refseqR versions 1.1.4 dated 2024-08-18 and 1.1.5 dated 2024-10-29
DESCRIPTION | 6 +- MD5 | 34 +++++++------- R/refseq_AAmol_wt.R | 3 - R/refseq_GeneID.R | 5 +- R/refseq_RNA2protein.R | 4 - R/refseq_description.R | 2 R/refseq_geneSymbol.R | 3 - R/refseq_protein2RNA.R | 4 - inst/doc/refseqR.R | 49 ++++++++++---------- inst/doc/refseqR.Rmd | 15 +++--- inst/doc/refseqR.html | 109 +++++++++++++++------------------------------- man/refseq_AAmol_wt.Rd | 3 - man/refseq_GeneID.Rd | 5 +- man/refseq_RNA2protein.Rd | 2 man/refseq_description.Rd | 2 man/refseq_geneSymbol.Rd | 3 - man/refseq_protein2RNA.Rd | 2 vignettes/refseqR.Rmd | 15 +++--- 18 files changed, 119 insertions(+), 147 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.18.2 dated 2024-08-28 and 3.20 dated 2024-10-29
DESCRIPTION | 64 ++++++++++++++++++++++++++++++++------------------ MD5 | 60 ++++++++++++++++++++++++---------------------- NEWS | 41 ++++++++++++++++++++++++++++++++ R/AUC.R | 6 ++-- R/Boyce.R | 9 +++---- R/Dsquared.R | 5 ++- R/applyThreshold.R | 8 +++--- R/errorMeasures.R |only R/getThreshold.R | 6 ++-- R/inputMunch.R | 10 ++++++- R/optiPair.R | 14 +++++----- R/optiThresh.R | 6 ++-- R/predDensity.R | 16 ++++++------ R/predPlot.R | 8 +++--- R/similarity.R | 8 +++--- R/threshMeasures.R | 8 +++--- man/AUC.Rd | 3 +- man/Boyce.Rd | 5 ++- man/Dsquared.Rd | 5 ++- man/RMSE.Rd | 4 +-- man/applyThreshold.Rd | 5 ++- man/errorMeasures.Rd |only man/getThreshold.Rd | 3 +- man/inputMunch.Rd | 5 ++- man/modEvA-package.Rd | 4 +-- man/optiPair.Rd | 7 +++-- man/optiThresh.Rd | 6 +++- man/predDensity.Rd | 18 +++++++------- man/predPlot.Rd | 3 +- man/quantReclass.Rd | 4 +-- man/similarity.Rd | 7 +++-- man/threshMeasures.Rd | 9 +++---- 32 files changed, 221 insertions(+), 136 deletions(-)
Title: Sampling from a Empirical Likelihood Bayesian Posterior of
Parameters Using Hamiltonian Monte Carlo
Description: A tool to draw samples from a Empirical Likelihood Bayesian posterior
of parameters using Hamiltonian Monte Carlo.
Author: Dang Trung Kien [aut],
Sanjay Chaudhuri [aut, cre],
Neo Han Wei, [aut]
Maintainer: Sanjay Chaudhuri <schaudhuri2@unl.edu>
Diff between elhmc versions 1.2.0 dated 2024-08-25 and 1.2.1 dated 2024-10-29
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 17 - R/ELHMC.R | 620 +++++++++++++++++++++++++++++------------------------------ R/ELU.R | 4 man/ELHMC.Rd | 8 6 files changed, 334 insertions(+), 333 deletions(-)
Title: Linked Inference of Genomic Experimental Relationships
Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Author: Joshua Welch [aut],
Yichen Wang [aut, cre],
Chao Gao [aut],
Jialin Liu [aut],
Joshua Sodicoff [aut, ctb],
Velina Kozareva [aut, ctb],
Evan Macosko [aut, ctb],
Paul Hoffman [ctb],
Ilya Korsunsky [ctb],
Robert Lee [ctb],
Andrew Robbins [ctb]
Maintainer: Yichen Wang <wayichen@umich.edu>
Diff between rliger versions 2.0.1 dated 2024-04-04 and 2.1.0 dated 2024-10-29
rliger-2.0.1/rliger/inst/doc/liger-vignette.R |only rliger-2.0.1/rliger/inst/doc/liger-vignette.Rmd |only rliger-2.0.1/rliger/inst/doc/liger-vignette.html |only rliger-2.0.1/rliger/src/cinmf_util.cpp |only rliger-2.0.1/rliger/vignettes/liger-vignette.Rmd |only rliger-2.1.0/rliger/DESCRIPTION | 10 rliger-2.1.0/rliger/MD5 | 218 +-- rliger-2.1.0/rliger/NAMESPACE | 16 rliger-2.1.0/rliger/NEWS.md | 24 rliger-2.1.0/rliger/R/ATAC.R | 20 rliger-2.1.0/rliger/R/DEG_marker.R | 1058 ++++++++++++-- rliger-2.1.0/rliger/R/GSEA.R | 137 + rliger-2.1.0/rliger/R/RcppExports.R | 32 rliger-2.1.0/rliger/R/cINMF.R | 3 rliger-2.1.0/rliger/R/classConversion.R | 1132 +++++++++++----- rliger-2.1.0/rliger/R/classes.R | 126 - rliger-2.1.0/rliger/R/clustering.R | 375 +++-- rliger-2.1.0/rliger/R/data.R | 66 rliger-2.1.0/rliger/R/deprecated.R | 4 rliger-2.1.0/rliger/R/dotplot.R | 8 rliger-2.1.0/rliger/R/downsample.R | 2 rliger-2.1.0/rliger/R/embedding.R | 52 rliger-2.1.0/rliger/R/factorMarker.R | 4 rliger-2.1.0/rliger/R/ggplotting.R | 147 +- rliger-2.1.0/rliger/R/h5Utility.R | 13 rliger-2.1.0/rliger/R/heatmap.R | 9 rliger-2.1.0/rliger/R/import.R | 152 +- rliger-2.1.0/rliger/R/integration.R | 446 +++++- rliger-2.1.0/rliger/R/liger-methods.R | 10 rliger-2.1.0/rliger/R/mergeObject.R | 1 rliger-2.1.0/rliger/R/preprocess.R | 258 +++ rliger-2.1.0/rliger/R/rliger-package.R |only rliger-2.1.0/rliger/R/subsetObject.R | 2 rliger-2.1.0/rliger/R/util.R | 123 - rliger-2.1.0/rliger/R/visualization.R | 597 +++++++- rliger-2.1.0/rliger/README.md | 19 rliger-2.1.0/rliger/build/partial.rdb |only rliger-2.1.0/rliger/build/vignette.rds |binary rliger-2.1.0/rliger/data/deg.marker.rda |only rliger-2.1.0/rliger/data/deg.pw.rda |only rliger-2.1.0/rliger/inst/doc/liger_vignette.R |only rliger-2.1.0/rliger/inst/doc/liger_vignette.Rmd |only rliger-2.1.0/rliger/inst/doc/liger_vignette.html |only rliger-2.1.0/rliger/inst/extdata/ligerToH5AD.R |only rliger-2.1.0/rliger/man/alignFactors.Rd |only rliger-2.1.0/rliger/man/calcARI.Rd | 8 rliger-2.1.0/rliger/man/calcAgreement.Rd | 26 rliger-2.1.0/rliger/man/calcAlignment.Rd | 10 rliger-2.1.0/rliger/man/calcNMI.Rd |only rliger-2.1.0/rliger/man/calcPurity.Rd | 3 rliger-2.1.0/rliger/man/centroidAlign.Rd |only rliger-2.1.0/rliger/man/createLiger.Rd | 16 rliger-2.1.0/rliger/man/deg.marker.Rd |only rliger-2.1.0/rliger/man/deg.pw.Rd |only rliger-2.1.0/rliger/man/dot-ggCellViolin.Rd | 4 rliger-2.1.0/rliger/man/dot-ggScatter.Rd | 9 rliger-2.1.0/rliger/man/dot-ggplotLigerTheme.Rd | 44 rliger-2.1.0/rliger/man/exportInteractTrack.Rd | 2 rliger-2.1.0/rliger/man/figures |only rliger-2.1.0/rliger/man/getFactorMarkers.Rd | 4 rliger-2.1.0/rliger/man/imputeKNN.Rd | 12 rliger-2.1.0/rliger/man/liger-DEG.Rd | 221 ++- rliger-2.1.0/rliger/man/liger-class.Rd | 19 rliger-2.1.0/rliger/man/ligerDataset-class.Rd | 38 rliger-2.1.0/rliger/man/ligerToSeurat.Rd | 22 rliger-2.1.0/rliger/man/linkGenesAndPeaks.Rd | 2 rliger-2.1.0/rliger/man/louvainCluster-deprecated.Rd | 2 rliger-2.1.0/rliger/man/makeInteractTrack-deprecated.Rd | 2 rliger-2.1.0/rliger/man/makeRiverplot-deprecated.Rd | 2 rliger-2.1.0/rliger/man/normalize.Rd | 17 rliger-2.1.0/rliger/man/online_iNMF-deprecated.Rd | 14 rliger-2.1.0/rliger/man/optimizeALS-deprecated.Rd | 2 rliger-2.1.0/rliger/man/plotBarcodeRank.Rd |only rliger-2.1.0/rliger/man/plotCellViolin.Rd | 54 rliger-2.1.0/rliger/man/plotClusterGeneViolin.Rd |only rliger-2.1.0/rliger/man/plotDensityDimRed.Rd | 27 rliger-2.1.0/rliger/man/plotDimRed.Rd | 82 + rliger-2.1.0/rliger/man/plotEnhancedVolcano.Rd |only rliger-2.1.0/rliger/man/plotGODot.Rd |only rliger-2.1.0/rliger/man/plotGeneLoadings.Rd | 54 rliger-2.1.0/rliger/man/plotGroupClusterDimRed.Rd | 42 rliger-2.1.0/rliger/man/plotHeatmap.Rd | 31 rliger-2.1.0/rliger/man/plotMarkerHeatmap.Rd | 53 rliger-2.1.0/rliger/man/plotPairwiseDEGHeatmap.Rd |only rliger-2.1.0/rliger/man/plotProportion.Rd | 64 rliger-2.1.0/rliger/man/plotProportionBox.Rd |only rliger-2.1.0/rliger/man/plotSpatial.Rd | 58 rliger-2.1.0/rliger/man/plotViolin.Rd | 60 rliger-2.1.0/rliger/man/plotVolcano.Rd | 74 - rliger-2.1.0/rliger/man/quantileAlignSNF.Rd | 4 rliger-2.1.0/rliger/man/quantileNorm.Rd | 30 rliger-2.1.0/rliger/man/quantile_norm-deprecated.Rd | 4 rliger-2.1.0/rliger/man/read10X.Rd | 32 rliger-2.1.0/rliger/man/read10XFiles.Rd |only rliger-2.1.0/rliger/man/readLiger.Rd | 31 rliger-2.1.0/rliger/man/readSubset.Rd | 2 rliger-2.1.0/rliger/man/rliger-deprecated.Rd | 6 rliger-2.1.0/rliger/man/rliger-package.Rd |only rliger-2.1.0/rliger/man/runCINMF.Rd | 43 rliger-2.1.0/rliger/man/runCluster.Rd | 9 rliger-2.1.0/rliger/man/runGOEnrich.Rd | 18 rliger-2.1.0/rliger/man/runGeneralQC.Rd | 68 rliger-2.1.0/rliger/man/runINMF.Rd | 40 rliger-2.1.0/rliger/man/runIntegration.Rd | 10 rliger-2.1.0/rliger/man/runOnlineINMF.Rd | 73 - rliger-2.1.0/rliger/man/runTSNE.Rd | 12 rliger-2.1.0/rliger/man/runUINMF.Rd | 24 rliger-2.1.0/rliger/man/runUMAP.Rd | 14 rliger-2.1.0/rliger/man/scaleNotCenter.Rd | 20 rliger-2.1.0/rliger/man/selectGenes.Rd | 16 rliger-2.1.0/rliger/man/updateLigerObject.Rd |only rliger-2.1.0/rliger/man/writeH5.Rd | 13 rliger-2.1.0/rliger/src/RcppExports.cpp | 109 + rliger-2.1.0/rliger/src/centoidAlign.cpp |only rliger-2.1.0/rliger/src/data_processing.cpp | 141 + rliger-2.1.0/rliger/tests/testthat/test_downstream.R | 94 + rliger-2.1.0/rliger/tests/testthat/test_factorization.R | 87 + rliger-2.1.0/rliger/tests/testthat/test_object.R | 5 rliger-2.1.0/rliger/tests/testthat/test_preprocessing.R | 1 rliger-2.1.0/rliger/tests/testthat/test_visualization.R | 40 rliger-2.1.0/rliger/vignettes/liger_vignette.Rmd |only 121 files changed, 5461 insertions(+), 1627 deletions(-)
More information about PublicWorksFinanceIT at CRAN
Permanent link
Title: 'GPU'/CPU Benchmarking in Debian-Based Systems
Description: 'GPU'/CPU Benchmarking on Debian-package based systems
This package benchmarks performance of a few standard linear algebra
operations (such as a matrix product and QR, SVD and LU decompositions)
across a number of different 'BLAS' libraries as well as a 'GPU' implementation.
To do so, it takes advantage of the ability to 'plug and play' different
'BLAS' implementations easily on a Debian and/or Ubuntu system. The current
version supports
- 'Reference BLAS' ('refblas') which are un-accelerated as a baseline
- Atlas which are tuned but typically configure single-threaded
- Atlas39 which are tuned and configured for multi-threaded mode
- 'Goto Blas' which are accelerated and multi-threaded
- 'Intel MKL' which is a commercial accelerated and multithreaded version.
As for 'GPU' computing, we use the CRAN package
- 'gputools'
For 'Goto Blas', the 'gotoblas2-helper' script from the ISM in Tokyo can be
used. For 'Intel MKL' we use the Revolution R packages from Ubuntu 9.10.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between gcbd versions 0.2.6 dated 2016-09-28 and 0.2.7 dated 2024-10-29
ChangeLog | 41 +++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++++------ MD5 | 19 ++++++++++--------- NAMESPACE | 2 +- README.md | 3 ++- build/vignette.rds |binary inst/doc/gcbd.Rnw | 9 +++------ inst/doc/gcbd.pdf |binary man/figures.Rd | 6 ------ vignettes/auto |only vignettes/gcbd.Rnw | 9 +++------ 11 files changed, 70 insertions(+), 35 deletions(-)
Title: 'DEXi' Decision Tree Analysis and Visualization
Description: Provides a versatile toolkit for analyzing and visualizing 'DEXi' (Decision EXpert for education)
decision trees, facilitating multi-criteria decision analysis directly within R. Users can
read .dxi files, manipulate decision trees, and evaluate various scenarios. It supports sensitivity
analysis through Monte Carlo simulations, one-at-a-time approaches, and variance-based
methods, helping to discern the impact of input variations. Additionally, it includes functionalities
for generating sampling plans and an array of visualization options for decision trees and
analysis results. A distinctive feature is the synoptic table plot, aiding in the efficient
comparison of scenarios. Whether for in-depth decision modeling or sensitivity analysis, this
package stands as a comprehensive solution. Definition of sensitivity analyses available in
Carpani, Bergez and Monod (2012) <doi:10.1016/j.envsoft.2011.10.002> and detailed description of the package soon available in Alaphilippe, Allart, [...truncated...]
Author: Roland Allart [aut],
Jacques-Eric Bergez [aut] ,
Marta Carpani [aut],
Herve Monod [aut] ,
Aude Alaphilippe [ctb] ,
Nicolas Cavan [ctb, cre],
INRAE [cph] )
Maintainer: Nicolas Cavan <nicolas.cavan@inrae.fr>
Diff between dexisensitivity versions 1.0.0 dated 2024-10-25 and 1.0.1 dated 2024-10-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 +++++++--- tests/testthat/test-aov.R | 2 +- tests/testthat/test-node.R | 4 ++-- tests/testthat/test-option.R | 1 + 6 files changed, 19 insertions(+), 14 deletions(-)
More information about dexisensitivity at CRAN
Permanent link
Title: Bayesian Screening and Variable Selection
Description: Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.
Author: Dongjin Li [aut, cre],
Debarshi Chakraborty [aut],
Somak Dutta [aut],
Vivekananda Roy [ctb]
Maintainer: Dongjin Li <liyangxiaobei@gmail.com>
Diff between bravo versions 3.2.1 dated 2024-05-13 and 3.2.2 dated 2024-10-29
DESCRIPTION | 24 ++++++++++++++++++++---- MD5 | 6 +++--- R/xzsven_notemp.R | 2 +- R/xzsven_temp.R | 2 +- 4 files changed, 25 insertions(+), 9 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@ucsd.edu>
Diff between bio3d versions 2.4-4 dated 2022-10-26 and 2.4-5 dated 2024-10-29
DESCRIPTION | 6 MD5 | 132 +++++++++--------- NEWS.md | 3 R/check.utility.R | 29 ++-- R/cnapath.R | 11 + R/plot.dccm.R | 4 build/vignette.rds |binary inst/CITATION | 23 ++- inst/doc/bio3d_vignettes.html | 258 ++++++++++++++++++++++++++++++++++--- man/aa.index.Rd | 18 +- man/as.pdb.Rd | 2 man/atom2ele.Rd | 5 man/atom2mass.Rd | 5 man/binding.site.Rd | 11 + man/bio3d.package.Rd | 4 man/biounit.Rd | 6 man/bounds.sse.Rd | 6 man/chain.pdb.Rd | 6 man/clean.pdb.Rd | 6 man/cna.Rd | 7 + man/cnapath.Rd | 7 + man/com.Rd | 5 man/community.tree.Rd | 6 man/dccm.gnm.Rd | 6 man/dccm.nma.Rd | 6 man/dccm.pca.Rd | 5 man/dccm.xyz.Rd | 10 + man/dm.Rd | 7 + man/dssp.Rd | 2 man/example.data.Rd | 20 +- man/fit.xyz.Rd | 13 + man/geostas.Rd | 5 man/get.pdb.Rd | 6 man/mask.dccm.Rd | 5 man/motif.find.Rd | 6 man/network.amendment.Rd | 6 man/nma.Rd | 6 man/nma.pdbs.Rd | 6 man/orient.pdb.Rd | 6 man/pca.xyz.Rd | 6 man/pdb.annotate.Rd | 5 man/pdb2sse.Rd | 6 man/plot.bio3d.Rd | 12 + man/plot.cna.Rd | 6 man/read.crd.amber.Rd | 2 man/read.crd.charmm.Rd | 2 man/read.fasta.pdb.Rd | 5 man/read.pdcBD.Rd | 6 man/read.pqr.Rd | 5 man/read.prmtop.Rd | 6 man/rgyr.Rd | 6 man/rmsd.Rd | 5 man/struct.aln.Rd | 7 + man/torsion.pdb.Rd | 6 man/torsion.xyz.Rd | 5 man/write.crd.Rd | 2 man/write.fasta.Rd | 6 man/write.pdb.Rd | 6 man/write.pir.Rd | 6 man/write.pqr.Rd | 5 src/Makevars | 1 tests/testthat/test-aanma.pdbs.R | 2 tests/testthat/test-get.seq.R | 6 tests/testthat/test-pdb.annotate.R | 6 tests/testthat/test-read.all.R | 4 tests/testthat/test-read.ncdf.R | 4 tests/testthat/test-seqaln.R | 4 67 files changed, 670 insertions(+), 147 deletions(-)
Title: Forward Stepwise Discriminant Analysis with Pillai's Trace
Description: A novel forward stepwise discriminant analysis framework
that integrates Pillai's trace with Uncorrelated Linear Discriminant Analysis (ULDA),
providing an improvement over traditional stepwise LDA methods that rely on Wilks' Lambda.
A stand-alone ULDA implementation is also provided, offering a more general solution
than the one available in the 'MASS' package. It automatically handles missing values and
provides visualization tools. For more details, see Wang (2024) <doi:10.48550/arXiv.2409.03136>.
Author: Siyu Wang [aut, cre, cph]
Maintainer: Siyu Wang <iamwangsiyu@gmail.com>
Diff between folda versions 0.1.0 dated 2024-09-11 and 0.2.0 dated 2024-10-29
folda-0.1.0/folda/man/forwardSel.Rd |only folda-0.1.0/folda/man/getBestVar.Rd |only folda-0.1.0/folda/man/getDesignMatrix.Rd |only folda-0.1.0/folda/man/getDownSampleInd.Rd |only folda-0.1.0/folda/man/getLDscores.Rd |only folda-0.1.0/folda/man/getNumFlag.Rd |only folda-0.1.0/folda/man/nonConstInd.Rd |only folda-0.2.0/folda/DESCRIPTION | 8 folda-0.2.0/folda/MD5 | 46 - folda-0.2.0/folda/NAMESPACE | 3 folda-0.2.0/folda/NEWS.md | 8 folda-0.2.0/folda/R/folda.R | 47 +- folda-0.2.0/folda/R/forwardSel.R | 12 folda-0.2.0/folda/R/plot.R | 55 +- folda-0.2.0/folda/R/utils.R | 175 ++++++- folda-0.2.0/folda/README.md | 30 - folda-0.2.0/folda/build/vignette.rds |binary folda-0.2.0/folda/inst/doc/folda.R | 27 + folda-0.2.0/folda/inst/doc/folda.Rmd | 57 ++ folda-0.2.0/folda/inst/doc/folda.html | 304 ++++++++----- folda-0.2.0/folda/man/checkPriorAndMisClassCost.Rd | 12 folda-0.2.0/folda/man/figures/README-unnamed-chunk-6-1.png |only folda-0.2.0/folda/man/folda.Rd | 9 folda-0.2.0/folda/man/getChiSqStat.Rd |only folda-0.2.0/folda/man/getMode.Rd | 17 folda-0.2.0/folda/tests/testthat/test-folda.R | 18 folda-0.2.0/folda/tests/testthat/test-plot.R |only folda-0.2.0/folda/tests/testthat/test-utils.R | 9 folda-0.2.0/folda/vignettes/folda.Rmd | 57 ++ 29 files changed, 683 insertions(+), 211 deletions(-)
Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad
Networks
Description: Many tools for making, modifying, mapping, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.2.6 dated 2024-10-05 and 1.3.1 dated 2024-10-29
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Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal
Target Variables
Description: The ordinal forest (OF) method allows ordinal regression with high-dimensional
and low-dimensional data. After having constructed an OF prediction rule using a training dataset,
it can be used to predict the values of the ordinal target variable for new observations.
Moreover, by means of the (permutation-based) variable importance measure of OF, it is also
possible to rank the covariates with respect to their importance in the prediction of the
values of the ordinal target variable.
OF is presented in Hornung (2020).
NOTE: Starting with package version 2.4, it is also possible to obtain class probability
predictions in addition to the class point predictions. Moreover, the variable importance values
can also be based on the class probability predictions. Preliminary results indicate that
this might lead to a better discrimination between influential and non-influential covariates.
The main functions of the package are: ordfor() (construction of OF) and predict.ordfor()
(prediction of [...truncated...]
Author: Roman Hornung [aut, cre]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between ordinalForest versions 2.4-3 dated 2022-11-30 and 2.4-4 dated 2024-10-29
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- R/ordfor.R | 2 +- build/partial.rdb |binary 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 3.0.0 dated 2024-09-18 and 3.0.1 dated 2024-10-29
nlmixr2extra-3.0.0/nlmixr2extra/man/backwardSearch.Rd |only nlmixr2extra-3.0.0/nlmixr2extra/man/covarSearchAuto.Rd |only nlmixr2extra-3.0.0/nlmixr2extra/man/forwardSearch.Rd |only nlmixr2extra-3.0.1/nlmixr2extra/DESCRIPTION | 6 +++--- nlmixr2extra-3.0.1/nlmixr2extra/MD5 | 11 ++++------- nlmixr2extra-3.0.1/nlmixr2extra/NAMESPACE | 3 --- nlmixr2extra-3.0.1/nlmixr2extra/NEWS.md | 4 ++++ nlmixr2extra-3.0.1/nlmixr2extra/R/SCM.R | 6 +++--- 8 files changed, 14 insertions(+), 16 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. In addition, offers a group penalty that provides consistent variable selection across quantiles. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre],
Shaobo Li [aut],
Adam Maidman [aut]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 4.1.1 dated 2024-06-04 and 4.1.2 dated 2024-10-29
DESCRIPTION | 17 ++++-- MD5 | 36 ++++++------- NEWS | 7 ++ R/gqCvPen.R | 12 ++-- R/gqPen.R | 11 +++- R/mainFunctions.R | 118 ++++++++++++++++++++++++++++++++++++------- R/rqPen.R | 2 R/utils.R | 6 +- R/workHorse.R | 85 +++++++++++++++++++++++++----- README.md | 9 ++- build/partial.rdb |binary man/predict.qic.select.Rd | 6 +- man/predict.rq.pen.seq.Rd | 3 + man/predict.rq.pen.seq.cv.Rd | 9 +++ man/rq.group.pen.Rd | 4 - man/rq.lasso.fit.Rd | 2 man/rq.nc.fit.Rd | 2 man/rq.pen.Rd | 8 +- man/rqPen.Rd | 7 ++ 19 files changed, 267 insertions(+), 77 deletions(-)
Title: Render Sequence Plots using 'ggplot2'
Description: A set of wrapper functions that mainly re-produces most of the
sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base
R to produce the plots this library draws on 'ggplot2'.
The plots are produced on the basis of a sequence object defined
with TraMineR::seqdef(). The package automates the reshaping and plotting
of sequence data. Resulting plots are of class 'ggplot', i.e. components
can be added and tweaked using '+' and regular 'ggplot2' functions.
Author: Marcel Raab [aut, cre]
Maintainer: Marcel Raab <marcel.raab@gmail.com>
Diff between ggseqplot versions 0.8.4 dated 2024-05-17 and 0.8.5 dated 2024-10-29
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/ggseqdplot.R | 4 ++-- R/ggseqeplot.R | 4 ++-- R/ggseqfplot.R | 5 ++++- R/ggseqiplot.R | 14 +++++++------- R/ggseqmsplot.R | 2 +- R/ggseqmtplot.R | 2 +- R/ggseqrfplot.R | 6 +++--- R/ggseqrplot.R | 2 +- R/ggseqtrplot.R | 36 +++++++++++++++++++++++++++++++++++- README.md | 22 ++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggseqplot.html | 40 ++++++++++++++++++++-------------------- 16 files changed, 113 insertions(+), 68 deletions(-)
Title: Optimal Nonparametric Testing of Missing Completely at Random
Description: Provides functions for carrying out nonparametric hypothesis tests of the MCAR hypothesis based on the theory of Frechet classes and compatibility. Also gives functions for computing halfspace representations of the marginal polytope and related geometric objects.
Author: Thomas B. Berrett [aut, cre] ,
Alberto Bordino [aut],
Danat Duisenbekov [aut],
Sean Jaffe [aut],
Richard J. Samworth [aut]
Maintainer: Thomas B. Berrett <tom.berrett@warwick.ac.uk>
Diff between MCARtest versions 1.2.1 dated 2024-03-22 and 1.2.2 dated 2024-10-29
DESCRIPTION | 38 ++++++++++++++++++++++++++++++++------ MD5 | 10 +++++----- NAMESPACE | 1 - R/get_SigmaS.R | 6 ++---- build/partial.rdb |binary man/get_SigmaS.Rd | 1 - 6 files changed, 39 insertions(+), 17 deletions(-)
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.5 dated 2024-08-20 and 1.6.6 dated 2024-10-29
DESCRIPTION | 7 ++---- MD5 | 38 +++++++++++++++++----------------- NAMESPACE | 1 R/aft.R | 6 ++--- R/pm2-3.R | 12 ++++++++-- R/vuniroot.R | 5 +++- inst/doc/Introduction.pdf |binary inst/doc/SimpleGuide.pdf |binary inst/doc/equations.pdf |binary inst/doc/multistate.pdf |binary inst/doc/predictnl.pdf |binary inst/working_code.R | 51 ++++++++++++++++++++++++++++++++++++++++++++++ inst/working_code.max | 31 +++++++++++++++++++++++++++ man/numDeltaMethod.Rd | 12 +++++++++- man/predictnl.Rd | 5 ---- man/voptimize.Rd | 2 - src/aft.cpp | 2 - src/c_optim.cpp | 2 - src/test-nmmin.cpp | 8 ++----- src/vuniroot.cpp | 3 +- 20 files changed, 139 insertions(+), 46 deletions(-)
Title: Extra Features for 'reactable' Package
Description: Enhanced functionality for 'reactable' in 'shiny' applications, offering interactive and dynamic data table capabilities with ease.
With 'reactable.extras', easily integrate a range of functions and components to enrich your 'shiny' apps and facilitate user-friendly data exploration.
Author: Recle Vibal [aut, cre],
Ivan Hrychaniuk [aut],
Andres Quintero [aut],
Pedro Silva [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Recle Vibal <opensource+recle@appsilon.com>
Diff between reactable.extras versions 0.2.0 dated 2023-11-23 and 0.2.1 dated 2024-10-29
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/inputs.R | 2 +- R/reactable-server.R | 3 +-- README.md | 4 ++-- man/figures/logo.png |binary man/reactable-extras-server.Rd | 3 +-- tests/testthat/test-inputs.R | 6 ++++++ 9 files changed, 27 insertions(+), 18 deletions(-)
More information about reactable.extras at CRAN
Permanent link
Title: R Commander Plugin for (Industrial) Design of Experiments
Description: Provides a platform-independent GUI for design of experiments. The package is implemented as a plugin to the R-Commander, which is a more general graphical user interface for statistics in R based on tcl/tk. DoE functionality can be accessed through the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping [aut, cre],
Fox John [ctb]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between RcmdrPlugin.DoE versions 0.12-5 dated 2023-10-07 and 0.12-6 dated 2024-10-29
DESCRIPTION | 17 ++++++----------- MD5 | 12 ++++++------ inst/NEWS | 5 +++++ man/Menu.FrF2level.Rd | 2 +- man/Menu.FrF2levelTab1.Rd | 2 +- man/Menus.Rd | 2 +- man/RcmdrPlugin.DoEUndocumentedFunctions.Rd | 9 ++++----- 7 files changed, 24 insertions(+), 25 deletions(-)
More information about RcmdrPlugin.DoE at CRAN
Permanent link
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.9.1 dated 2024-08-23 and 1.10.0 dated 2024-10-29
DESCRIPTION | 6 MD5 | 34 +-- R/microtable.R | 106 +++++++---- R/trans_abund.R | 4 R/trans_alpha.R | 163 +++++++++++------- R/trans_beta.R | 61 ++++-- R/trans_diff.R | 378 ++++++++++++++++-------------------------- R/trans_env.R | 42 +++- R/trans_func.R | 7 R/trans_network.R | 98 +++++++--- data/prok_func_FAPROTAX.RData |binary man/microtable.Rd | 42 ++-- man/trans_abund.Rd | 4 man/trans_alpha.Rd | 50 +++-- man/trans_beta.Rd | 12 - man/trans_diff.Rd | 63 ++----- man/trans_env.Rd | 5 man/trans_network.Rd | 17 + 18 files changed, 580 insertions(+), 512 deletions(-)
Title: Utility Functions, Datasets and Extended Examples for Survival
Analysis
Description: Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Author: Annika Tillander [ctb],
Andreas Karlsson [aut],
Johan Zetterqvist [ctb],
Peter Strom [ctb],
Benedicte Delcoigne [ctb],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between biostat3 versions 0.2.1 dated 2024-08-19 and 0.2.2 dated 2024-10-29
DESCRIPTION | 8 MD5 | 180 +-- NAMESPACE | 3 R/bshazard.R |only R/muhaz2.R | 28 R/poisson.ci.R | 49 build/partial.rdb |binary inst/doc/labs/_extensions |only inst/doc/labs/local_server.R |only inst/doc/labs/q1.html | 2125 +++++++++++++++++++++++++++++++++---- inst/doc/labs/q1.qmd |only inst/doc/labs/q10.html | 2196 ++++++++++++++++++++++++++++++++++---- inst/doc/labs/q10.qmd |only inst/doc/labs/q11.html | 2051 +++++++++++++++++++++++++++++++++-- inst/doc/labs/q11.qmd |only inst/doc/labs/q12.html | 2077 +++++++++++++++++++++++++++++++++--- inst/doc/labs/q12.qmd |only inst/doc/labs/q13.html | 2045 +++++++++++++++++++++++++++++++++-- inst/doc/labs/q13.qmd |only inst/doc/labs/q14.html | 2226 ++++++++++++++++++++++++++++++++++---- inst/doc/labs/q14.qmd |only inst/doc/labs/q2.html | 2121 +++++++++++++++++++++++++++++++++---- inst/doc/labs/q2.qmd |only inst/doc/labs/q2.rmarkdown |only inst/doc/labs/q22.html | 2180 +++++++++++++++++++++++++++++++++----- inst/doc/labs/q22.qmd |only inst/doc/labs/q23.html | 2194 ++++++++++++++++++++++++++++++++++---- inst/doc/labs/q23.qmd |only inst/doc/labs/q25.html | 2101 +++++++++++++++++++++++++++++++++--- inst/doc/labs/q25.qmd |only inst/doc/labs/q28.html | 2191 ++++++++++++++++++++++++++++++++++---- inst/doc/labs/q28.qmd |only inst/doc/labs/q28.rmarkdown |only inst/doc/labs/q3.html | 2084 +++++++++++++++++++++++++++++++++--- inst/doc/labs/q3.qmd |only inst/doc/labs/q4.html | 2062 +++++++++++++++++++++++++++++++++--- inst/doc/labs/q4.qmd |only inst/doc/labs/q6.html | 2160 +++++++++++++++++++++++++++++++++---- inst/doc/labs/q6.qmd |only inst/doc/labs/q7.Rmd | 2 inst/doc/labs/q7.html | 2458 ++++++++++++++++++++++++++++++++++--------- inst/doc/labs/q7.qmd |only inst/doc/labs/q8.html | 2157 +++++++++++++++++++++++++++++++++---- inst/doc/labs/q8.qmd |only inst/doc/labs/q9.html | 2212 +++++++++++++++++++++++++++++++++----- inst/doc/labs/q9.qmd |only inst/doc/local_server.R |only inst/doc/q1.R | 16 inst/doc/q10.R | 121 +- inst/doc/q11.R | 28 inst/doc/q12.R | 24 inst/doc/q13.R | 2 inst/doc/q14.R | 21 inst/doc/q2.R | 164 +- inst/doc/q22.R | 47 inst/doc/q23.R | 61 - inst/doc/q25.R | 121 +- inst/doc/q28.R | 74 - inst/doc/q3.R | 96 + inst/doc/q4.R | 31 inst/doc/q6.R | 80 - inst/doc/q7.R | 337 +++-- inst/doc/q7_work.R |only inst/doc/q8.R | 111 + inst/doc/q9.R | 143 +- inst/doc/solutions/q1.Rmd | 14 inst/doc/solutions/q1.html | 734 +++++++++++- inst/doc/solutions/q1.qmd | 31 inst/doc/solutions/q10.Rmd | 25 inst/doc/solutions/q10.html | 687 +++++++----- inst/doc/solutions/q11.html | 233 ++-- inst/doc/solutions/q12.html | 245 ++-- inst/doc/solutions/q13.html | 181 +-- inst/doc/solutions/q14.html | 468 ++++---- inst/doc/solutions/q2.Rmd | 40 inst/doc/solutions/q2.html | 1327 +++++++++++++++++++---- inst/doc/solutions/q22.html | 650 +++++++---- inst/doc/solutions/q23.Rmd | 8 inst/doc/solutions/q23.html | 1186 +++++++++++++++++--- inst/doc/solutions/q25.Rmd | 4 inst/doc/solutions/q25.html | 703 +++++++++--- inst/doc/solutions/q28.Rmd | 32 inst/doc/solutions/q28.html | 635 ++++++----- inst/doc/solutions/q3.Rmd | 6 inst/doc/solutions/q3.html | 304 +++-- inst/doc/solutions/q4.Rmd | 4 inst/doc/solutions/q4.html | 1451 ++++++++++++++++++++++--- inst/doc/solutions/q6.Rmd | 25 inst/doc/solutions/q6.html | 2144 +++++++++++++++++++++++++++++++++---- inst/doc/solutions/q7.Rmd | 37 inst/doc/solutions/q7.html | 1121 +++++++++++++------ inst/doc/solutions/q8.Rmd | 7 inst/doc/solutions/q8.html | 954 +++++++++++----- inst/doc/solutions/q9.Rmd | 2 inst/doc/solutions/q9.html | 557 +++++---- man/bshazard.Rd |only man/poisson.ci.Rd | 14 97 files changed, 44315 insertions(+), 7901 deletions(-)
Title: Tools for Interactive Data Exploration
Description: Tools for interactive data exploration built using 'shiny'. Includes apps for descriptive
statistics, visualizing probability distributions, inferential statistics, linear regression,
logistic regression and RFM analysis.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between xplorerr versions 0.1.2 dated 2021-05-21 and 0.2.0 dated 2024-10-29
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Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions.
Provides access to 'RStudio' public repositories at
<https://packagemanager.posit.co>, and transparent management of
system requirements without administrative privileges. Currently supported
distributions are 'CentOS' / 'RHEL' 7-9, and several 'RHEL' derivatives
('Rocky Linux', 'AlmaLinux', 'Oracle Linux', and 'Amazon Linux'),
'openSUSE' / 'SLES' 15.4-5, 'Debian' 11-12, and 'Ubuntu' LTS 20-22.
Author: Inaki Ucar [aut, cph, cre] ,
R Core Team [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between rspm versions 0.6.0 dated 2024-06-21 and 0.6.1 dated 2024-10-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/zzz_debian_base.R | 3 ++- README.md | 1 + 5 files changed, 14 insertions(+), 8 deletions(-)
Title: Collection of Methods Constructed using Kernel-Based Quadratic
Distances
Description: It includes test for multivariate normality, test for uniformity on the d-dimensional
Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson
kernel-based density and clustering algorithm for spherical data. For more information see
Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024)
<doi:10.48550/arXiv.2402.02290>
Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>,
Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>,
and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Author: Giovanni Saraceno [aut, cre] ,
Marianthi Markatou [aut],
Raktim Mukhopadhyay [aut],
Mojgan Golzy [aut]
Maintainer: Giovanni Saraceno <gsaracen@buffalo.edu>
Diff between QuadratiK versions 1.1.1 dated 2024-06-05 and 1.1.2 dated 2024-10-29
QuadratiK-1.1.1/QuadratiK/man/summary-kb.test-method.Rd |only QuadratiK-1.1.1/QuadratiK/man/summary-pk.test-method.Rd |only QuadratiK-1.1.2/QuadratiK/DESCRIPTION | 37 QuadratiK-1.1.2/QuadratiK/MD5 | 162 +- QuadratiK-1.1.2/QuadratiK/NAMESPACE | 26 QuadratiK-1.1.2/QuadratiK/NEWS.md |only QuadratiK-1.1.2/QuadratiK/R/QuadratiK-package.R | 106 + QuadratiK-1.1.2/QuadratiK/R/RcppExports.R | 28 QuadratiK-1.1.2/QuadratiK/R/breast_cancer.R | 3 QuadratiK-1.1.2/QuadratiK/R/classes.R | 17 QuadratiK-1.1.2/QuadratiK/R/clustering_functions.R | 575 ++++++---- QuadratiK-1.1.2/QuadratiK/R/critical_value.R | 36 QuadratiK-1.1.2/QuadratiK/R/h_selection.R | 151 ++ QuadratiK-1.1.2/QuadratiK/R/kb.test.R | 248 +++- QuadratiK-1.1.2/QuadratiK/R/pk.test.R | 116 +- QuadratiK-1.1.2/QuadratiK/R/pkbd_functions.R | 125 +- QuadratiK-1.1.2/QuadratiK/R/utility.R | 45 QuadratiK-1.1.2/QuadratiK/R/wine.R | 4 QuadratiK-1.1.2/QuadratiK/R/wireless.R | 7 QuadratiK-1.1.2/QuadratiK/README.md | 90 + QuadratiK-1.1.2/QuadratiK/build/vignette.rds |binary QuadratiK-1.1.2/QuadratiK/inst/CITATION |only QuadratiK-1.1.2/QuadratiK/inst/doc/Introduction.R |only QuadratiK-1.1.2/QuadratiK/inst/doc/Introduction.Rmd |only QuadratiK-1.1.2/QuadratiK/inst/doc/Introduction.html |only QuadratiK-1.1.2/QuadratiK/inst/doc/TwoSample_test.R | 30 QuadratiK-1.1.2/QuadratiK/inst/doc/TwoSample_test.Rmd | 106 + QuadratiK-1.1.2/QuadratiK/inst/doc/TwoSample_test.html | 236 ++-- QuadratiK-1.1.2/QuadratiK/inst/doc/generate_rpkb.R | 9 QuadratiK-1.1.2/QuadratiK/inst/doc/generate_rpkb.Rmd | 51 QuadratiK-1.1.2/QuadratiK/inst/doc/generate_rpkb.html | 67 - QuadratiK-1.1.2/QuadratiK/inst/doc/kSample_test.R | 36 QuadratiK-1.1.2/QuadratiK/inst/doc/kSample_test.Rmd | 124 +- QuadratiK-1.1.2/QuadratiK/inst/doc/kSample_test.html | 214 ++- QuadratiK-1.1.2/QuadratiK/inst/doc/uniformity.R | 34 QuadratiK-1.1.2/QuadratiK/inst/doc/uniformity.Rmd | 95 + QuadratiK-1.1.2/QuadratiK/inst/doc/uniformity.html | 122 ++ QuadratiK-1.1.2/QuadratiK/inst/doc/wireless_clustering.R | 23 QuadratiK-1.1.2/QuadratiK/inst/doc/wireless_clustering.Rmd | 66 - QuadratiK-1.1.2/QuadratiK/inst/doc/wireless_clustering.html | 117 +- QuadratiK-1.1.2/QuadratiK/man/DOF.Rd | 44 QuadratiK-1.1.2/QuadratiK/man/DOF_norm.Rd | 46 QuadratiK-1.1.2/QuadratiK/man/QuadratiK-package.Rd | 174 +-- QuadratiK-1.1.2/QuadratiK/man/breast_cancer.Rd | 73 - QuadratiK-1.1.2/QuadratiK/man/compute_CV.Rd | 102 + QuadratiK-1.1.2/QuadratiK/man/cv_ksample.Rd | 84 - QuadratiK-1.1.2/QuadratiK/man/dpkb.Rd | 205 ++- QuadratiK-1.1.2/QuadratiK/man/generate_SN.Rd | 66 - QuadratiK-1.1.2/QuadratiK/man/kb.test-class.Rd | 115 +- QuadratiK-1.1.2/QuadratiK/man/kb.test.Rd | 452 +++++-- QuadratiK-1.1.2/QuadratiK/man/normal_CV.Rd | 78 - QuadratiK-1.1.2/QuadratiK/man/pk.test-class.Rd | 98 - QuadratiK-1.1.2/QuadratiK/man/pk.test.Rd | 189 ++- QuadratiK-1.1.2/QuadratiK/man/pkbc-class.Rd | 56 QuadratiK-1.1.2/QuadratiK/man/pkbc.Rd | 272 ++-- QuadratiK-1.1.2/QuadratiK/man/pkbc_validation.Rd | 166 +- QuadratiK-1.1.2/QuadratiK/man/plot.pkbc.Rd | 42 QuadratiK-1.1.2/QuadratiK/man/poisson_CV.Rd | 80 - QuadratiK-1.1.2/QuadratiK/man/predict.pkbc.Rd | 91 - QuadratiK-1.1.2/QuadratiK/man/sample_hypersphere.Rd | 46 QuadratiK-1.1.2/QuadratiK/man/select_h.Rd | 68 + QuadratiK-1.1.2/QuadratiK/man/stats_clusters.Rd | 94 - QuadratiK-1.1.2/QuadratiK/man/summary.kb.test.Rd |only QuadratiK-1.1.2/QuadratiK/man/summary.pk.test.Rd |only QuadratiK-1.1.2/QuadratiK/man/summary.pkbc.Rd | 60 - QuadratiK-1.1.2/QuadratiK/man/var_k.Rd | 46 QuadratiK-1.1.2/QuadratiK/man/var_norm.Rd | 46 QuadratiK-1.1.2/QuadratiK/man/var_two.Rd | 42 QuadratiK-1.1.2/QuadratiK/man/wine.Rd | 110 - QuadratiK-1.1.2/QuadratiK/man/wireless.Rd | 107 - QuadratiK-1.1.2/QuadratiK/src/RcppExports.cpp | 18 QuadratiK-1.1.2/QuadratiK/src/kernel_function.cpp | 36 QuadratiK-1.1.2/QuadratiK/tests/testthat/Rplots.pdf |binary QuadratiK-1.1.2/QuadratiK/tests/testthat/test-dpkb.R | 65 + QuadratiK-1.1.2/QuadratiK/tests/testthat/test-kb.test.R | 43 QuadratiK-1.1.2/QuadratiK/tests/testthat/test-pk.test.R | 26 QuadratiK-1.1.2/QuadratiK/tests/testthat/test-pkbc.R | 166 ++ QuadratiK-1.1.2/QuadratiK/tests/testthat/test-rpkb.R | 31 QuadratiK-1.1.2/QuadratiK/tests/testthat/test-sample_hypersphere.R | 4 QuadratiK-1.1.2/QuadratiK/tests/testthat/test-select_h.R | 55 QuadratiK-1.1.2/QuadratiK/tests/testthat/test-validation.R | 4 QuadratiK-1.1.2/QuadratiK/vignettes/Introduction.Rmd |only QuadratiK-1.1.2/QuadratiK/vignettes/TwoSample_test.Rmd | 106 + QuadratiK-1.1.2/QuadratiK/vignettes/generate_rpkb.Rmd | 51 QuadratiK-1.1.2/QuadratiK/vignettes/kSample_test.Rmd | 124 +- QuadratiK-1.1.2/QuadratiK/vignettes/uniformity.Rmd | 95 + QuadratiK-1.1.2/QuadratiK/vignettes/wireless_clustering.Rmd | 66 - 87 files changed, 4759 insertions(+), 2289 deletions(-)
Title: High-Dimensional Temporal Disaggregation
Description: Provides tools for temporal disaggregation, including:
(1) High-dimensional and low-dimensional series generation for simulation studies;
(2) A toolkit for temporal disaggregation and benchmarking using low-dimensional indicator series
as proposed by Dagum and Cholette (2006, ISBN:978-0-387-35439-2);
(3) Novel techniques by Mosley, Gibberd, and Eckley (2022, <doi:10.1111/rssa.12952>)
for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.
Author: Kaveh Salehzadeh Nobari [aut, cre],
Luke Mosley [aut]
Maintainer: Kaveh Salehzadeh Nobari <k.salehzadeh-nobari@imperial.ac.uk>
Diff between DisaggregateTS versions 2.0.0 dated 2022-05-30 and 3.0.0 dated 2024-10-29
DESCRIPTION | 50 +++-- MD5 | 67 ++++--- NAMESPACE | 1 R/ARcov.R | 24 +- R/ARcov_lit.R | 32 ++- R/TempDisaggDGP.R | 394 +++++++++++++++++----------------------------- R/chowlin.R | 149 ++++++++--------- R/chowlin_likelihood.R | 71 +++----- R/data.R |only R/disaggregate.R | 310 ++++++++++++++++++------------------ R/hdBIC.R | 49 +++-- R/kindex.R | 33 ++- R/refit.R | 41 +++- R/simulDiagnosis.R |only R/sptd.R | 210 +++++++++++------------- R/sptd_BIC.R | 80 ++++----- build/partial.rdb |binary build/vignette.rds |only data |only inst/REFERENCES.bib | 216 +++++++++++++++++++++---- inst/doc |only man/ARcov.Rd | 12 + man/ARcov_lit.Rd | 12 + man/TempDisaggDGP.Rd | 70 +++----- man/chowlin.Rd | 36 +--- man/chowlin_likelihood.Rd | 24 +- man/combined_data.Rd |only man/disaggregate.Rd | 32 +-- man/hdBIC.Rd | 18 +- man/k.index.Rd | 17 + man/refit.Rd | 12 - man/simulDiagnosis.Rd |only man/sptd.Rd | 35 +--- man/sptd_BIC.Rd | 25 +- tests |only vignettes |only 36 files changed, 1083 insertions(+), 937 deletions(-)
More information about DisaggregateTS at CRAN
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Title: Quickly Build and Manipulate Financial Networks
Description: Providing classes, methods, and functions to deal with financial networks.
Users can easily store information about both physical and legal persons by using pre-made classes that are studied for integration with scraping packages such as 'rvest' and 'RSelenium'.
Moreover, the package assists in creating various types of financial networks depending on the type of relation between its units depending on the relation under scrutiny (ownership, board interlocks, etc.), the desired tie type (valued or binary), and renders them in the most common formats (adjacency matrix, incidence matrix, edge list, 'igraph', 'network').
There are also ad-hoc functions for the Fiedler value, global network efficiency, and cascade-failure analysis.
Author: Fabio Ashtar Telarico [aut, cre]
Maintainer: Fabio Ashtar Telarico <Fabio-Ashtar.Telarico@fdv.uni-lj.si>
Diff between FinNet versions 0.1.2 dated 2023-08-10 and 0.2 dated 2024-10-29
DESCRIPTION | 14 MD5 | 96 ++-- NAMESPACE | 18 R/00.helpers.R | 685 ++++++++++++++++++++++++++++++- R/04.FF_both.R | 14 R/04.FF_either.R | 40 - R/05.1.graph_methods.R | 24 - R/05.1.network_methods.R | 173 +++++++ R/05.network&graph.R | 10 R/06.1.Fielder.R |only R/06.2.Efficiency.R |only R/06.3.cfa.R |only R/FinNet-package.R |only R/RcppExports.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/analysis_examples.R |only inst/doc/analysis_examples.Rmd |only inst/doc/analysis_examples.html |only inst/doc/workflow-igraph_financial.R | 2 inst/doc/workflow-igraph_financial.html | 8 inst/doc/workflow-network_financial.R |only inst/doc/workflow-network_financial.Rmd |only inst/doc/workflow-network_financial.html |only man/FF.Rd | 12 man/FF.binary.both.Rd | 13 man/FF.binary.management.Rd | 13 man/FF.binary.ownership.Rd | 13 man/FF.naive.both.Rd | 12 man/FF.naive.management.Rd | 12 man/FF.naive.ownership.Rd | 12 man/FF.norm.both.Rd | 13 man/FF.norm.management.Rd | 12 man/FF.norm.ownership.Rd | 12 man/FinNet.Rd |only man/SCC.Rd |only man/SCC2.Rd |only man/SCC2.prep.Rd |only man/cfa.Rd |only man/dot-set_names.Rd | 8 man/extract.matrix.Rd |only man/fiedler.Rd |only man/fun-igraph_financial.Rd | 16 man/fun-network_financial.Rd |only man/get.matrix.adjacency.Rd | 8 man/get.matrix.adjacency.both.Rd | 8 man/get.net.Rd | 2 man/igraph_E_iterators.Rd | 2 man/igraph_v_iterators.Rd | 2 man/is.neither.null.nor.na.Rd | 2 man/is.null.na.Rd | 2 man/load.Matrix.Rd |only man/naming.Rd | 2 man/network.efficiency.Rd |only man/network_operators.Rd |only man/plot_igraph-methods.Rd | 4 man/plot_network-methods.Rd |only man/show-network_financial-method.Rd | 12 man/show_network_financial.Rd | 12 src |only vignettes/analysis_examples.Rmd |only vignettes/workflow-network_financial.Rmd |only 62 files changed, 1138 insertions(+), 150 deletions(-)
Title: Machine Learning and Inference for Topological Data Analysis
Description: Topological data analysis is a powerful tool for finding non-linear global structure
in whole datasets. The main tool of topological data analysis is persistent homology, which computes
a topological shape descriptor of a dataset called a persistence diagram. 'TDApplied' provides
useful and efficient methods for analyzing groups of persistence diagrams with machine learning and statistical inference,
and these functions can also interface with other data science packages to form flexible and integrated
topological data analysis pipelines.
Author: Shael Brown [aut, cre],
Dr. Reza Farivar [aut, fnd]
Maintainer: Shael Brown <shaelebrown@gmail.com>
Diff between TDApplied versions 3.0.3 dated 2024-03-12 and 3.0.4 dated 2024-10-29
DESCRIPTION | 10 MD5 | 43 +- NAMESPACE | 3 NEWS.md | 5 R/bootstrap.R | 94 +++- R/distance_calculations.R | 2 R/enclosing_rad.R |only R/inference.R | 675 +++++++++++++++++++++++++++++++- R/machine_learning.R | 2 R/rips_complexes.R | 16 README.md | 27 - build/partial.rdb |binary inst/doc/ML_and_Inference.R | 128 +++++- inst/doc/ML_and_Inference.Rmd | 212 +++++++++- inst/doc/ML_and_Inference.html | 305 ++++++++++++-- man/bootstrap_persistence_thresholds.Rd | 5 man/diagram_ksvm.Rd | 2 man/enclosing_radius.Rd |only man/permutation_model_inference.Rd |only man/universal_null.Rd |only tests/testthat/test-enclosing.R |only tests/testthat/test-inference.R | 100 ++++ tests/testthat/test-rips.R | 2 vignettes/ML_and_Inference.Rmd | 212 +++++++++- vignettes/REFERENCES.bib | 10 25 files changed, 1710 insertions(+), 143 deletions(-)
Title: Stochastic Frontier Analysis Routines
Description: Maximum likelihood estimation for stochastic frontier
analysis (SFA) of production (profit) and cost functions. The package
includes the basic stochastic frontier for cross-sectional or pooled
data with several distributions for the one-sided error term (i.e.,
Rayleigh, gamma, Weibull, lognormal, uniform, generalized exponential
and truncated skewed Laplace), the latent class stochastic frontier
model (LCM) as described in Dakpo et al. (2021)
<doi:10.1111/1477-9552.12422>, for cross-sectional and pooled data,
and the sample selection model as described in Greene (2010)
<doi:10.1007/s11123-009-0159-1>, and applied in Dakpo et al. (2021)
<doi:10.1111/agec.12683>. Several possibilities in terms of
optimization algorithms are proposed.
Author: K Herve Dakpo [aut, cre],
Yann Desjeux [aut],
Arne Henningsen [aut],
Laure Latruffe [aut]
Maintainer: K Herve Dakpo <k-herve.dakpo@inrae.fr>
Diff between sfaR versions 1.0.0 dated 2023-07-04 and 1.0.1 dated 2024-10-29
DESCRIPTION | 8 MD5 | 68 NAMESPACE | 250 - NEWS.md | 7 R/data.R | 18 R/deprecated.R | 736 ++-- R/extract.R | 264 - R/sfaR-package.R | 2 R/sfalcmcross-halfnormal-2Classes.R | 1998 +++++----- R/sfalcmcross-halfnormal-3Classes.R | 2964 ++++++++-------- R/sfalcmcross-halfnormal-4Classes.R | 4146 +++++++++++----------- R/sfalcmcross-halfnormal-5Classes.R | 5540 +++++++++++++++--------------- R/sfalcmcross.R | 1808 ++++----- R/sfaselectioncross-hnormal.R | 6574 ++++++++++++++++++------------------ R/zzz.R | 31 man/dairynorway.Rd | 78 man/dairyspain.Rd | 98 man/efficiencies.Rd | 678 +-- man/electricity.Rd | 2 man/extract.Rd | 132 man/fitted.Rd | 126 man/ic.Rd | 140 man/logLik.Rd | 144 man/residuals.Rd | 150 man/ricephil.Rd | 4 man/sfaR-deprecated.Rd | 518 +- man/sfaR-package.Rd | 2 man/sfalcmcross.Rd | 918 ++--- man/sfaselectioncross.Rd | 1200 +++--- man/summary.Rd | 320 - man/swissrailways.Rd | 98 man/utility.Rd | 2 man/vcov.Rd | 248 - man/worldprod.Rd | 2 tests/sfacross.Rout.save | 24 35 files changed, 14663 insertions(+), 14635 deletions(-)
Title: Data Mining Classification and Regression Methods
Description: Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.8 improved help, several warning and error code fixes (more stable version, all examples run correctly); 1.4.7 improved Importance function and examples, minor error fixes; 1.4.6 / 1.4.5 / 1.4.4 new automated machine learning (AutoML) and ensembles, via improved fit(), mining() and mparheuristic() functions, and new categorical preprocessing, via improved delevels() function; 1.4.3 new metrics (e.g., macro precision, explained variance), new "lssvm" model and improved mparheuristic() function; 1.4.2 new "NMAE" metric, "xgboost" and "cv.glmnet" models (16 classification and 18 regression models); 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vect [...truncated...]
Author: Paulo Cortez [aut, cre]
Maintainer: Paulo Cortez <pcortez@dsi.uminho.pt>
Diff between rminer versions 1.4.7 dated 2024-10-23 and 1.4.8 dated 2024-10-29
DESCRIPTION | 8 - MD5 | 18 ++-- R/model.R | 229 ++++++++++++++++++++++++++------------------------- R/plots.R | 35 +++++-- R/preprocess.R | 2 man/Importance.Rd | 1 man/fit.Rd | 9 +- man/imputation.Rd | 2 man/mining.Rd | 1 man/mparheuristic.Rd | 17 +++ 10 files changed, 177 insertions(+), 145 deletions(-)
Title: Routing with 'GTFS' (General Transit Feed Specification) Data
Description: Use 'GTFS' (General Transit Feed Specification) data for routing
from nominated start and end stations, for extracting 'isochrones', and
travel times from any nominated start station to all other stations.
Author: Mark Padgham [aut, cre],
Marcin Stepniak [aut] ,
Alexandra Kapp [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between gtfsrouter versions 0.1.2 dated 2023-09-23 and 0.1.3 dated 2024-10-29
DESCRIPTION | 10 +++--- MD5 | 56 ++++++++++++++++++------------------- NEWS.md | 8 +++++ R/extract-gtfs.R | 6 +-- R/frequencies_to_stop_times.R | 8 +++++ R/go_home_work.R | 30 +++++++++++++++---- R/route-headway.R | 21 ++++++++++++- R/transfers.R | 11 +++---- R/traveltimes.R | 4 +- R/utils.R | 14 ++++++--- README.md | 31 ++++++++------------ build/vignette.rds |binary inst/doc/gtfsrouter.R | 4 +- inst/doc/gtfsrouter.html | 36 +++++++++-------------- inst/doc/transfers.html | 18 +++++++---- inst/doc/traveltimes.html | 8 ++--- man/berlin_gtfs_to_zip.Rd | 6 +++ man/frequencies_to_stop_times.Rd | 8 +++++ man/gtfs_route_headway.Rd | 7 ++++ man/gtfs_traveltimes.Rd | 4 +- man/gtfsrouter.Rd | 2 - man/process_gtfs_local.Rd | 16 ++++++++++ tests/testthat/test-extract.R | 47 +++++++++++++++---------------- tests/testthat/test-frequencies.R | 14 ++++----- tests/testthat/test-go-home.R | 4 +- tests/testthat/test-route.R | 32 ++++++++++----------- tests/testthat/test-time-formats.R | 12 +++---- tests/testthat/test-transfers.R | 2 - tests/testthat/test-traveltimes.R | 2 - 29 files changed, 254 insertions(+), 167 deletions(-)
Title: Center of Gravity Methods
Description: Implementation of the Centre of Gravity method and the Extrapolated Centre of Gravity method. It supports replicated observations.
Cameron, D.G., et al (1982) <doi:10.1366/0003702824638610>
JCGM (2008) <doi:10.59161/JCGM100-2008E>.
Author: Hugo Gasca-Aragon [aut, cre]
Maintainer: Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>
Diff between ECG versions 0.5.1 dated 2024-10-22 and 0.5.2 dated 2024-10-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/plot.CGr.R | 2 +- man/assess.CGdata.Rd | 4 +++- man/assess.CGr.Rd | 2 +- man/assess.ECGdata.Rd | 3 ++- man/assess.ECGr.Rd | 2 +- man/plot.ECGdata.Rd | 12 ++++++++++-- 8 files changed, 29 insertions(+), 18 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include a) Phillip J. Paine, Simon P. Preston, Michail Tsagris and Andrew T. A. Wood (2018).
"An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere".
Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020).
"Spherical regression models with general covariates and anisotropic errors".
Statistics and Computing 30(1): 153--165. < [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 6.8 dated 2024-09-09 and 6.9 dated 2024-10-29
DESCRIPTION | 22 ++++++----- MD5 | 76 ++++++++++++++++++++++----------------- NAMESPACE | 2 - R/bic.mixpkbd.R |only R/bic.mixspcauchy.R |only R/bic.mixvmf.R | 19 ++++----- R/dmixpkbd.R |only R/dmixscpauchy.R |only R/mixpkbd.mle.R |only R/mixspcauchy.mle.R |only R/mixvmf.mle.R | 10 ++--- R/pk2.R |only R/pkbd2test.R | 86 +++++++-------------------------------------- R/rmixpkbd.R |only R/rmixspcauchy.R |only R/sp2.R |only R/spcauchy2test.R | 86 +++++++-------------------------------------- man/Directional-package.Rd | 6 +-- man/bic.mixvmf.Rd | 35 +++++++++++++----- man/colwatsons.Rd | 2 - man/dirda.Rd | 7 +-- man/dirda.cv.Rd | 4 +- man/dmixvmf.Rd | 17 ++++++-- man/dsespc.Rd | 2 - man/dvm.Rd | 2 - man/dvmf.Rd | 8 ++-- man/iag.reg.Rd | 2 - man/mixvmf.mle.Rd | 34 ++++++++++++----- man/nsmedian.Rd | 2 - man/pc.test.Rd | 2 - man/rayleigh.Rd | 2 - man/read.fbm.Rd | 2 - man/rmixvmf.Rd | 20 ++++++---- man/rvmf.Rd | 4 +- man/sespc.mle.Rd | 4 +- man/sespc.reg.Rd | 8 ++-- man/spcauchy2test.Rd | 34 ++++++++++++++--- man/spher.sespc.contour.Rd | 2 - man/spher.vmf.contour.Rd | 8 ++-- man/spml.mle.Rd | 2 - man/spml.reg.Rd | 2 - man/vmf.contour.Rd | 12 +++--- man/vmf.mle.Rd | 7 +-- man/vmfreg.Rd | 5 +- 44 files changed, 246 insertions(+), 290 deletions(-)
Title: QTL Mapping for Multi Parent Populations
Description: For Multi Parent Populations (MPP) Identity By Descend (IBD)
probabilities are computed using Hidden Markov Models. These probabilities
are then used in a mixed model approach for QTL Mapping as described in
Li et al. (<doi:10.1007/s00122-021-03919-7>).
Author: Martin Boer [aut] ,
Wenhao Li [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenMPP versions 1.0.2 dated 2022-12-02 and 1.0.3 dated 2024-10-29
DESCRIPTION | 31 MD5 | 57 - NAMESPACE | 1 NEWS.md | 46 - R/createGDataMPPInternal.R | 4 R/createQTLMPP.R | 24 R/effectPlot.R | 8 R/scanQTL.R | 34 R/selQTLMPP.R | 3 R/statgenMPP.R | 4 R/utils.R | 8 README.md | 86 ++ build/partial.rdb |binary build/vignette.rds |binary data/barleyMQM.rda |binary data/barleyPheno.rda |binary data/maizeMQM.rda |binary data/maizeSQM.rda |binary inst/CITATION | 44 - inst/doc/QTLMapping_in_MultiParentPopulations.Rmd | 43 - inst/doc/QTLMapping_in_MultiParentPopulations.html | 752 +++++++++------------ inst/tinytest/ABC_MQM_max |binary man/figures |only man/plot.QTLMPP.Rd | 10 man/plot.gDataMPP.Rd | 2 man/scanQTL.Rd | 1 man/statgenMPP-package.Rd | 4 vignettes/QTLMapping_in_MultiParentPopulations.Rmd | 43 - vignettes/bibliography.bib | 497 +++++++------ 29 files changed, 843 insertions(+), 859 deletions(-)
Title: The LIC for T Distribution Regression Analysis
Description: This comprehensive toolkit for T-distributed regression is designated as "TLIC" (The LIC for T Distribution Regression Analysis) analysis. It is predicated on the assumption that the error term adheres to a T-distribution. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02664763.2022.2053949>.
Author: Guangbao Guo [aut, cre] ,
Guofu Jing [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between TLIC versions 0.2 dated 2024-09-25 and 0.3 dated 2024-10-29
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/TLIC.R | 7 ++++--- R/terr.R | 31 ++++++++++++------------------- man/TLIC.Rd | 4 ++-- man/terr.Rd | 25 ++++++++++--------------- 6 files changed, 38 insertions(+), 49 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.14.0 dated 2023-08-10 and 0.15.0 dated 2024-10-29
DESCRIPTION | 20 +++-- MD5 | 72 ++++++++++---------- NAMESPACE | 1 NEWS.md | 22 +++++- R/global_progression_handler.R | 20 +++++ R/handler_cli.R | 3 R/handler_filesize.R | 11 +++ R/handler_notifier.R | 25 +++--- R/handler_ntfy.R |only R/handler_rpushbullet.R | 26 ++----- R/handler_shiny.R | 12 +++ R/handlers.R | 6 + R/notifiers.R |only R/progressr-package.R | 8 +- R/with_progress.R | 8 +- build/vignette.rds |binary inst/doc/progressr-intro.html | 29 +++++++- inst/doc/progressr-intro.md | 33 ++++++++- man/figures/handler_cli-default.svg | 2 man/figures/handler_cli-format-1.svg | 2 man/figures/handler_pbcol-adjust-mid.svg | 2 man/figures/handler_pbcol-adjust-right-complete.svg | 2 man/figures/handler_pbcol-default.svg | 2 man/figures/handler_pbmcapply-default.svg | 2 man/figures/handler_progress-complete.svg | 2 man/figures/handler_progress-default.svg | 2 man/figures/handler_progress-format-1.svg | 2 man/figures/handler_progress-format-2.svg | 2 man/figures/handler_txtprogressbar-char-ansi.svg | 2 man/figures/handler_txtprogressbar-char-width-2.svg | 2 man/figures/handler_txtprogressbar-char.svg | 2 man/figures/handler_txtprogressbar-default.svg | 2 man/figures/handler_txtprogressbar-style-1.svg | 2 man/figures/handler_txtprogressbar-style-3.svg | 2 man/handler_ntfy.Rd |only man/progressr.Rd | 20 +++++ man/with_progress.Rd | 6 + tests/handler_filesize.R |only vignettes/progressr-intro.md | 33 ++++++++- 39 files changed, 279 insertions(+), 108 deletions(-)
Title: Data Augmentation for Private Posterior Estimation
Description: A data augmentation based sampler for conducting privacy-aware Bayesian inference. The dapper_sample()
function takes an existing sampler as input and automatically constructs
a privacy-aware sampler. The process of constructing a sampler is simplified
through the specification of four independent modules, allowing for
easy comparison between different privacy mechanisms by only swapping
out the relevant modules. Probability mass functions
for the discrete Gaussian and discrete Laplacian are provided to facilitate
analyses dealing with privatized count data. The output of dapper_sample()
can be analyzed using many of the same tools from the 'rstan' ecosystem. For methodological details
on the sampler see Ju et al. (2022) <doi:10.48550/arXiv.2206.00710>,
and for details on the discrete Gaussian and discrete Laplacian distributions see
Canonne et al. (2020) <doi:10.48550/arXiv.2004.00010>.
Author: Kevin Eng [aut, cre, cph]
Maintainer: Kevin Eng <kevine1221@gmail.com>
Diff between dapper versions 1.0.0 dated 2024-07-09 and 1.0.1 dated 2024-10-29
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/dapper_sample.R | 7 ++++--- R/discrete_gaussian.R | 5 +++-- R/privacy_class.R | 2 +- build/partial.rdb |binary man/dapper_sample.Rd | 4 ++-- man/ddnorm.Rd | 2 +- man/new_privacy.Rd | 2 +- 10 files changed, 32 insertions(+), 24 deletions(-)