Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-16 1.0
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Ben Goodrich [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph],
Juan Palacios [cph],
Jiang Yang [cph],
Gael Guennebaud [cph],
Jitse Niesen [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.15.5 dated 2019-12-09 and 2.16.0 dated 2020-02-03
DESCRIPTION | 10 MD5 | 399 +++---- NAMESPACE | 4 NEWS.md | 1 R/MxAlgebra.R | 2 R/MxAlgebraConvert.R | 2 R/MxAlgebraObjective.R | 2 R/MxApply.R | 2 R/MxBaseNamed.R | 2 R/MxCommunication.R | 2 R/MxCompare.R | 4 R/MxConstraint.R | 2 R/MxCycleDetection.R | 11 R/MxData.R | 16 R/MxDependencies.R | 2 R/MxDetectCores.R | 2 R/MxErrorHandling.R | 2 R/MxExpectationGREML.R | 2 R/MxExpectationLISREL.R | 30 R/MxExpectationNormal.R | 88 + R/MxExpectationRAM.R | 25 R/MxFitFunctionAlgebra.R | 2 R/MxLISRELModel.R | 27 R/MxMI.R | 2 R/MxMLObjective.R | 2 R/MxModel.R | 47 R/MxPath.R | 5 R/MxRAMModel.R | 2 R/MxRAMtoML.R | 2 R/MxRename.R | 1 R/MxRestore.R | 2 R/MxRowObjective.R | 2 R/MxRunHelperFunctions.R | 2 R/MxSummary.R | 59 - R/MxSwift.R | 2 R/MxUnitTesting.R | 2 R/MxVersion.R | 2 R/OriginalMx.R | 2 R/omxGetNPSOL.R | 2 demo/UnivariateTwinAnalysis_MatrixRaw.R | 2 inst/CITATION | 4 inst/models/nightly/CSOLNP_segfault_regression_test--unidentifed_EFA.R | 2 inst/models/nightly/ModificationIndexCheck.R | 2 inst/models/nightly/MultigroupRobustSE_test.R | 2 inst/models/nightly/MxTryHardTest.R | 2 inst/models/nightly/StateSpaceContinuous.R | 2 inst/models/nightly/startsTestMissing.R | 2 inst/models/passing/ACEDuplicateMatrices.R | 2 inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R | 2 inst/models/passing/Autoregressive_Tree_Matrix.R | 2 inst/models/passing/Autoregressive_Tree_Path.R | 2 inst/models/passing/BivRegStdTestSE.R | 2 inst/models/passing/BukinN2_regressiontest.R | 2 inst/models/passing/CheckpointingEveryIteration.R | 2 inst/models/passing/IntroSEM-BivariateRaw.R | 5 inst/models/passing/IntroSEM-OneFactorRaw.R | 2 inst/models/passing/LCAlazarsfeld-rewrite.R | 2 inst/models/passing/LCAlazarsfeld.R | 2 inst/models/passing/LISRELFactorRegression_Matrix.R | 8 inst/models/passing/LisrelTypeCheck.R | 12 inst/models/passing/MxPath.R | 5 inst/models/passing/NameParameterOverlap.R | 2 inst/models/passing/NelderMeadTest--eqConstraint.R | 2 inst/models/passing/SanityTest.R | 2 inst/models/passing/StateSpaceOsc.R | 2 inst/models/passing/SummaryCheck.R | 2 inst/models/passing/cycle.R | 4 inst/models/passing/defvaralgebra.R | 2 inst/models/passing/dependentConstraintTest.R | 2 inst/models/passing/derivFilter.R | 2 inst/models/passing/ifa-lmp.R | 4 inst/models/passing/lmer-1.R | 2 inst/models/passing/redundantConstraintTest.R | 2 inst/models/passing/rfitfunc.R | 2 inst/models/passing/stdizedRAMpaths--UserProvidedCov.R | 2 inst/models/passing/testNumericDerivWithConstraintWarning.R | 2 inst/tools/testModels.R | 2 inst/tools/updateCopyright.sh | 2 man/MxModel-class.Rd | 24 man/OpenMx.Rd | 1 man/genericFitDependencies-MxBaseFitFunction-method.Rd | 4 man/imxCreateMatrix.Rd | 17 man/imxGenericModelBuilder.Rd | 12 man/imxGetSlotDisplayNames.Rd | 9 man/imxModelBuilder.Rd | 12 man/imxPPML.Test.Battery.Rd | 12 man/imxPPML.Test.Test.Rd | 9 man/mxAlgebra.Rd | 2 man/mxBootstrapEval.Rd | 2 man/mxCheckIdentification.Rd | 2 man/mxComputeCheckpoint.Rd | 25 man/mxComputeConfidenceInterval.Rd | 13 man/mxComputeEM.Rd | 20 man/mxComputeGradientDescent.Rd | 19 man/mxComputeIterate.Rd | 12 man/mxComputeLoadContext.Rd | 12 man/mxComputeLoadData.Rd | 23 man/mxComputeLoop.Rd | 13 man/mxComputeNewtonRaphson.Rd | 11 man/mxComputeNumericDeriv.Rd | 17 man/mxComputeOnce.Rd | 11 man/mxComputeSequence.Rd | 8 man/mxComputeStandardError.Rd | 3 man/mxComputeTryHard.Rd | 11 man/mxData.Rd | 26 man/mxDataWLS.Rd | 7 man/mxDescribeDataWLS.Rd | 7 man/mxEval.Rd | 2 man/mxExpectationBA81.Rd | 17 man/mxExpectationLISREL.Rd | 8 man/mxExpectationRAM.Rd | 15 man/mxFitFunctionML.Rd | 2 man/mxFitFunctionMultigroup.Rd | 2 man/mxMatrix.Rd | 2 man/mxRestore.Rd | 15 man/mxSE.Rd | 13 man/mxSave.Rd | 5 man/omxAugmentDataWithWLSSummary.Rd | 14 man/omxCheckEquals.Rd | 2 man/omxCheckIdentical.Rd | 2 man/omxCheckSetEquals.Rd | 2 man/omxCheckTrue.Rd | 2 man/omxCheckWithinPercentError.Rd | 2 man/omxManifestModelByParameterJacobian.Rd | 3 man/omxSetParameters.Rd | 2 src/AlgebraFunctions.h | 66 - src/Compute.cpp | 265 ++-- src/Compute.h | 6 src/ComputeGD.cpp | 46 src/ComputeNM.cpp | 32 src/ComputeNM.h | 2 src/ComputeNR.cpp | 6 src/Connectedness.h | 6 src/FellnerFitFunction.cpp | 10 src/LoadDataAPI.h | 11 src/MarkovExpectation.cpp | 2 src/MarkovFF.cpp | 12 src/RAMInternal.h | 7 src/asubnp.cpp | 8 src/ba81quad.cpp | 467 ++------ src/ba81quad.h | 505 ++++++-- src/dmvnorm.cpp | 30 src/finiteDifferences.h | 8 src/fitMultigroup.cpp | 10 src/glue.cpp | 36 src/matrix.cpp | 20 src/matrix.h | 24 src/omxAlgebra.cpp | 73 - src/omxAlgebra.h | 10 src/omxAlgebraFitFunction.cpp | 14 src/omxData.cpp | 562 ++++++---- src/omxData.h | 81 - src/omxDefines.h | 24 src/omxExpectation.cpp | 34 src/omxExpectation.h | 8 src/omxExpectationBA81.cpp | 50 src/omxExpectationBA81.h | 7 src/omxFIMLFitFunction.cpp | 20 src/omxFIMLFitFunction.h | 2 src/omxFitFunction.cpp | 35 src/omxFitFunction.h | 2 src/omxFitFunctionBA81.cpp | 29 src/omxGREMLExpectation.cpp | 18 src/omxGREMLExpectation.h | 6 src/omxGREMLfitfunction.cpp | 22 src/omxHessianCalculation.cpp | 8 src/omxImportFrontendState.cpp | 10 src/omxLISRELExpectation.cpp | 22 src/omxLISRELExpectation.h | 2 src/omxMLFitFunction.cpp | 28 src/omxMatrix.cpp | 47 src/omxMatrix.h | 21 src/omxNLopt.cpp | 6 src/omxNLopt.h | 2 src/omxNPSOLSpecific.cpp | 4 src/omxRAMExpectation.cpp | 152 +- src/omxRowFitFunction.cpp | 41 src/omxSadmvnWrapper.h | 10 src/omxState.cpp | 35 src/omxState.h | 10 src/omxStateSpaceExpectation.cpp | 2 src/omxWLSFitFunction.cpp | 11 src/path.h | 15 src/polynomial.h | 8 src/povRAM.cpp | 20 src/ssMLFit.cpp | 11 tests/testthat/test-ACELRTCI20160808.R | 2 tests/testthat/test-ConstantSubst.R | 2 tests/testthat/test-DataErrorDetection.R | 2 tests/testthat/test-GREML_Error_Detection.R | 2 tests/testthat/test-MatrixErrorDetection.R | 2 tests/testthat/test-ModelIdentification.R | 2 tests/testthat/test-cor.R |only tests/testthat/test-defvar.R | 2 tests/testthat/test-dmvnorm.R | 2 tests/testthat/test-ifa-drm1.R | 3 tests/testthat/test-mxBounds.R | 2 tests/testthat/test-mxsave.R | 2 tests/testthat/test-naAction.R |only tests/testthat/test-simplestCI.R | 2 tests/testthat/test-wls-binary.R |only tools/ifa-regression | 46 202 files changed, 2578 insertions(+), 1869 deletions(-)
Title: OPUS Miner Algorithm for Filtered Top-k Association Discovery
Description: Provides a simple R interface to the OPUS Miner algorithm (implemented in C++) for finding the top-k productive, non-redundant itemsets from transaction data. The OPUS Miner algorithm uses the OPUS search algorithm to efficiently discover the key associations in transaction data, in the form of self-sufficient itemsets, using either leverage or lift. See <http://i.giwebb.com/index.php/research/association-discovery/> for more information in relation to the OPUS Miner algorithm.
Author: Geoffrey I Webb [aut, cph] (OPUS Miner algorithm and C++
implementation,
http://i.giwebb.com/index.php/research/association-discovery/),
Christoph Bergmeir [ctb, cre],
Angus Dempster [ctb, cph] (R interface)
Maintainer: Christoph Bergmeir <christoph.bergmeir@monash.edu>
Diff between opusminer versions 0.1-0 dated 2017-02-16 and 0.1-1 dated 2020-02-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/opus_miner.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>,
David Barrios <metal@usal.es>,
Carlos Prieto <cprietos@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 1.1.23 dated 2019-11-09 and 1.1.24 dated 2020-02-03
DESCRIPTION | 8 MD5 | 18 R/barplot.R | 8 R/multigraph.R | 18 R/netcoin.R | 76 +-- build/vignette.rds |binary inst/doc/netCoin.R | 140 +++--- inst/doc/netCoin.html | 1083 ++++++++++++++++++++++++-------------------------- inst/doc/surCoin.R | 178 ++++---- inst/doc/surCoin.html | 907 ++++++++++++++++++++--------------------- 10 files changed, 1220 insertions(+), 1216 deletions(-)
Title: Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Description: Write 'YAML' front matter for R Markdown and related
documents. yml_*() functions write 'YAML' and use_*() functions let
you write the resulting 'YAML' to your clipboard or to .yml files
related to your project.
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>),
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
RStudio [cph, fnd]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ymlthis versions 0.1.1 dated 2019-11-18 and 0.1.2 dated 2020-02-03
DESCRIPTION | 8 MD5 | 42 +- NEWS.md | 5 R/use_yml.R | 2 R/yml_pagedown.R | 1 inst/WORDLIST | 1 inst/doc/introduction-to-ymlthis.html | 662 ++++++++++++++++----------------- inst/doc/yaml-fieldguide.html | 16 inst/doc/yaml-overview.html | 132 +++--- man/code_chunk.Rd | 2 man/draw_yml_tree.Rd | 4 man/includes2.Rd | 2 man/pagedown_business_card_template.Rd | 2 man/pkgdown_template.Rd | 2 man/yml.Rd | 10 man/yml_bookdown_opts.Rd | 2 man/yml_latex_opts.Rd | 6 man/yml_output.Rd | 4 man/yml_pagedown_opts.Rd | 3 man/yml_reference.Rd | 4 man/yml_replace.Rd | 10 man/yml_site_opts.Rd | 2 22 files changed, 464 insertions(+), 458 deletions(-)
Title: Streams of Random Numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.
Author: Josef Leydold <josef.leydold@wu.ac.at>
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between rstream versions 1.3.5 dated 2017-06-21 and 1.3.6 dated 2020-02-03
DESCRIPTION | 8 +- MD5 | 10 +- NEWS | 7 + inst/doc/rstream.pdf |binary man/rstream-package.Rd | 4 - src/RngStreams.c | 176 ++++++++++++++++++++++++++----------------------- 6 files changed, 112 insertions(+), 93 deletions(-)
Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more
accessible to students and professionals from Epidemiology and
Public Health related disciplines. Includes a function to report
coefficients and confidence intervals from models using robust
standard errors (when available), functions that expand 'ggplot2'
plots and functions relevant for introductory papers in Epidemiology
or Public Health. Please note that use of the
provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre],
Frank Harell [ctb],
John Fox [ctb],
R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>
Diff between pubh versions 1.1.3 dated 2019-12-10 and 1.1.5 dated 2020-02-03
DESCRIPTION | 20 MD5 | 51 - NAMESPACE | 3 R/data.R | 47 R/descriptive_functions.R | 64 + R/plot_functions.R | 24 data/Brenner.rda |binary data/Macmahon.rda |binary data/Roberts.rda |binary inst/doc/introduction.R | 53 - inst/doc/introduction.Rmd | 81 + inst/doc/introduction.html | 879 +++++++++++------- inst/doc/regression.R | 26 inst/doc/regression.Rmd | 30 inst/doc/regression.html | 738 +++++++-------- inst/rmarkdown/templates/report/skeleton/skeleton.Rmd | 6 man/Brenner.Rd | 10 man/Macmahon.Rd | 12 man/Roberts.Rd | 8 man/Rothman.Rd | 5 man/Sandler.Rd | 6 man/Vanderpump.Rd | 6 man/box_plot.Rd | 5 man/cross_tab.Rd |only man/hist_norm.Rd | 6 vignettes/introduction.Rmd | 81 + vignettes/regression.Rmd | 30 27 files changed, 1286 insertions(+), 905 deletions(-)
Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>),
Thanh Wang [ctb] (<https://orcid.org/0000-0002-5729-1908>)
Maintainer: Miao YU <yufreecas@gmail.com>
Diff between enviGCMS versions 0.5.7 dated 2019-08-22 and 0.6.0 dated 2020-02-03
DESCRIPTION | 16 +++---- MD5 | 92 ++++++++++++++++++++++------------------- NAMESPACE | 4 + NEWS.md | 15 ++++++ R/general.R | 36 ++++++++++++++++ R/getdata.R | 2 R/getmzrt.R | 42 +++++++++++++++++- R/io.R | 42 +++++------------- R/mda.R | 17 ++++--- R/peaks.R | 18 ++++---- R/plotmzrt.R | 28 +++++++++++- build/vignette.rds |binary inst/doc/GCMSDA.html | 7 +-- inst/doc/PooledQC.R |only inst/doc/PooledQC.Rmd |only inst/doc/PooledQC.html |only inst/shinyapps/MDPlot/server.R | 2 inst/shinyapps/MDPlot/ui.R | 2 inst/shinyapps/sccp/server.R | 2 man/GetIntegration.Rd | 13 ++++- man/Getisotopologues.Rd | 2 man/findohc.Rd | 14 ++++-- man/getareastd.Rd | 3 - man/getbgremove.Rd | 10 +++- man/getbiotechrep.Rd | 10 +++- man/getdata.Rd | 12 ++++- man/getdata2.Rd | 20 ++++++-- man/getdoe.Rd | 11 ++++ man/getdwtus.Rd |only man/getfeaturesanova.Rd | 14 +++++- man/getfeaturest.Rd | 3 - man/getfilter.Rd | 3 - man/getformula.Rd | 11 +++- man/getgrouprep.Rd | 10 +++- man/getmr.Rd | 10 +++- man/getmzrt.Rd | 12 ++++- man/getpower.Rd | 3 - man/getpqsi.Rd |only man/getsccp.Rd | 12 ++++- man/gettechrep.Rd | 10 +++- man/gettimegrouprep.Rd | 10 +++- man/getupload.Rd | 11 ++++ man/gifmr.Rd | 11 ++++ man/plotcc.Rd |only man/plotdwtus.Rd |only man/plotmr.Rd | 11 ++++ man/plotmrc.Rd | 3 - man/plotpca.Rd | 13 ++++- man/plotrsd.Rd | 3 - man/svaplot.Rd | 3 - vignettes/PooledQC.Rmd |only 51 files changed, 403 insertions(+), 170 deletions(-)
Title: Interactive Plotting for Mathematical Models of Infectious
Disease Spread
Description: Provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ordinary differential equation (ODE) models (such as the SIR, SIRS, and SIS models), or create their own. This latter flexibility allows 'shinySIR' to be applied to simple ODEs from any discipline. The package is a useful teaching tool as students can visualize how changing different parameters can impact model dynamics, with minimal knowledge of coding in R. The built-in models are inspired by those featured in Keeling and Rohani (2008) <doi:10.2307/j.ctvcm4gk0> and Bjornstad (2018) <doi:10.1007/978-3-319-97487-3>.
Author: Sinead E. Morris [aut, cre] (<https://orcid.org/0000-0001-8626-1698>),
Ottar N. Bjornstad [ctb]
Maintainer: Sinead E. Morris <sinead.morris@columbia.edu>
Diff between shinySIR versions 0.1.0 dated 2020-01-20 and 0.1.1 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NEWS.md | 7 +++++++ R/plotting.R | 9 ++++++--- R/run_shiny.R | 9 +++++++-- R/solving.R | 1 + inst/CITATION |only inst/doc/Vignette.R | 4 ++++ inst/doc/Vignette.Rmd | 16 +++++++++++++++- inst/doc/Vignette.html | 12 +++++++++++- man/plot_model.Rd | 9 ++++++++- man/run_shiny.Rd | 9 ++++++++- vignettes/Vignette.Rmd | 16 +++++++++++++++- 13 files changed, 98 insertions(+), 25 deletions(-)
Title: Read, Analyze and Plot River Networks
Description: Functions for reading, analysing and plotting river networks.
For this package, river networks consist of sections and nodes with associated attributes,
e.g. to characterise their morphological, chemical and biological state.
The package provides functions to read this data from text files, to analyse the network
structure and network paths and regions consisting of sections and nodes that fulfill
prescribed criteria, and to plot the river network and associated properties.
Author: Peter Reichert
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Diff between rivernet versions 1.2 dated 2019-03-08 and 1.2.1 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/analyze.rivernet.Rd | 3 --- man/rivernet-package.Rd | 7 +++++-- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.4 dated 2017-12-15 and 0.9.5 dated 2020-02-03
DESCRIPTION | 12 +-- MD5 | 32 +++++---- NAMESPACE | 9 ++ NEWS | 28 ++++---- R/IPW.R | 82 +++++++++++++++++++++++ R/T2.R |only R/WVC.R |only R/filters.R | 186 +++++++++++++++++++++++++++++++++++++++++++++++++++--- R/plsVarSel.R | 2 R/shaving.R | 4 - R/trunc.R | 2 man/T2_pls.Rd |only man/VIP.Rd | 22 ++++-- man/WVC_pls.Rd |only man/filterPLSR.Rd | 17 +++- man/ipw_pls.Rd | 15 +++- man/mcuve_pls.Rd | 3 man/shaving.Rd | 8 +- man/truncation.Rd | 2 19 files changed, 360 insertions(+), 64 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Arni Magnusson [aut] (<https://orcid.org/0000-0003-2769-6741>),
Hans Skaug [aut],
Anders Nielsen [aut] (<https://orcid.org/0000-0001-9683-9262>),
Casper Berg [aut] (<https://orcid.org/0000-0002-3812-5269>),
Kasper Kristensen [aut],
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Koen van Bentham [aut],
Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>),
Nafis Sadat [ctb] (<https://orcid.org/0000-0001-5715-616X>),
Daniel Lüdecke [ctb] (<https://orcid.org/0000-0002-8895-3206>),
Russ Lenth [ctb],
Mollie Brooks [aut, cre] (<https://orcid.org/0000-0001-6963-8326>)
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 0.2.3 dated 2019-01-11 and 1.0.0 dated 2020-02-03
glmmTMB-0.2.3/glmmTMB/R/tmbroot.R |only glmmTMB-0.2.3/glmmTMB/inst/doc/model_evaluation.html |only glmmTMB-0.2.3/glmmTMB/inst/doc/model_evaluation.rmd |only glmmTMB-0.2.3/glmmTMB/man/tmbroot.Rd |only glmmTMB-0.2.3/glmmTMB/vignettes/model_evaluation.rmd |only glmmTMB-1.0.0/glmmTMB/DESCRIPTION | 29 glmmTMB-1.0.0/glmmTMB/MD5 | 153 ++-- glmmTMB-1.0.0/glmmTMB/NAMESPACE | 18 glmmTMB-1.0.0/glmmTMB/R/Anova.R | 31 glmmTMB-1.0.0/glmmTMB/R/VarCorr.R | 39 - glmmTMB-1.0.0/glmmTMB/R/emmeans.R | 78 -- glmmTMB-1.0.0/glmmTMB/R/enum.R | 6 glmmTMB-1.0.0/glmmTMB/R/family.R | 84 +- glmmTMB-1.0.0/glmmTMB/R/glmmTMB.R | 326 ++++++---- glmmTMB-1.0.0/glmmTMB/R/methods.R | 298 ++++++--- glmmTMB-1.0.0/glmmTMB/R/predict.R | 94 ++ glmmTMB-1.0.0/glmmTMB/R/profile.R | 31 glmmTMB-1.0.0/glmmTMB/R/utils.R | 69 +- glmmTMB-1.0.0/glmmTMB/R/zzz.R |only glmmTMB-1.0.0/glmmTMB/build/vignette.rds |binary glmmTMB-1.0.0/glmmTMB/cleanup |only glmmTMB-1.0.0/glmmTMB/configure.ac |only glmmTMB-1.0.0/glmmTMB/inst/NEWS.Rd | 51 + glmmTMB-1.0.0/glmmTMB/inst/doc/add_link.md |only glmmTMB-1.0.0/glmmTMB/inst/doc/covstruct.R | 21 glmmTMB-1.0.0/glmmTMB/inst/doc/covstruct.html | 40 - glmmTMB-1.0.0/glmmTMB/inst/doc/covstruct.rmd | 46 - glmmTMB-1.0.0/glmmTMB/inst/doc/glmmTMB.R | 4 glmmTMB-1.0.0/glmmTMB/inst/doc/glmmTMB.Rnw | 6 glmmTMB-1.0.0/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.0.0/glmmTMB/inst/doc/mcmc.html | 15 glmmTMB-1.0.0/glmmTMB/inst/doc/miscEx.html | 7 glmmTMB-1.0.0/glmmTMB/inst/doc/model_evaluation.R | 179 ++++- glmmTMB-1.0.0/glmmTMB/inst/doc/model_evaluation.Rnw |only glmmTMB-1.0.0/glmmTMB/inst/doc/model_evaluation.pdf |only glmmTMB-1.0.0/glmmTMB/inst/doc/parallel.R |only glmmTMB-1.0.0/glmmTMB/inst/doc/parallel.Rmd |only glmmTMB-1.0.0/glmmTMB/inst/doc/parallel.html |only glmmTMB-1.0.0/glmmTMB/inst/doc/sim.html | 11 glmmTMB-1.0.0/glmmTMB/inst/doc/troubleshooting.R | 89 ++ glmmTMB-1.0.0/glmmTMB/inst/doc/troubleshooting.html | 132 +++- glmmTMB-1.0.0/glmmTMB/inst/doc/troubleshooting.rmd | 179 ++++- glmmTMB-1.0.0/glmmTMB/inst/other_methods/extract.R |only glmmTMB-1.0.0/glmmTMB/inst/other_methods/influence_mixed.R |only glmmTMB-1.0.0/glmmTMB/inst/test_data/make_ex.R |only glmmTMB-1.0.0/glmmTMB/inst/test_data/models.rda |only glmmTMB-1.0.0/glmmTMB/inst/test_data/oldfit.rds |only glmmTMB-1.0.0/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.0.0/glmmTMB/inst/vignette_data/plasma.rda |only glmmTMB-1.0.0/glmmTMB/inst/vignette_data/troubleshooting.rda |only glmmTMB-1.0.0/glmmTMB/man/Owls.Rd | 2 glmmTMB-1.0.0/glmmTMB/man/confint.glmmTMB.Rd | 43 + glmmTMB-1.0.0/glmmTMB/man/downstream_methods.Rd | 27 glmmTMB-1.0.0/glmmTMB/man/fbx.Rd | 6 glmmTMB-1.0.0/glmmTMB/man/fixef.Rd | 15 glmmTMB-1.0.0/glmmTMB/man/formFuns.Rd | 4 glmmTMB-1.0.0/glmmTMB/man/formatVC.Rd | 11 glmmTMB-1.0.0/glmmTMB/man/formula.glmmTMB.Rd | 3 glmmTMB-1.0.0/glmmTMB/man/getME.glmmTMB.Rd | 3 glmmTMB-1.0.0/glmmTMB/man/getReStruc.Rd | 4 glmmTMB-1.0.0/glmmTMB/man/get_cor.Rd | 12 glmmTMB-1.0.0/glmmTMB/man/glmmTMB.Rd | 157 ++-- glmmTMB-1.0.0/glmmTMB/man/glmmTMBControl.Rd | 34 - glmmTMB-1.0.0/glmmTMB/man/glmmTMB_methods.Rd |only glmmTMB-1.0.0/glmmTMB/man/mkTMBStruc.Rd | 45 + glmmTMB-1.0.0/glmmTMB/man/nbinom2.Rd | 37 - glmmTMB-1.0.0/glmmTMB/man/predict.glmmTMB.Rd | 23 glmmTMB-1.0.0/glmmTMB/man/print.VarCorr.glmmTMB.Rd | 9 glmmTMB-1.0.0/glmmTMB/man/profile.glmmTMB.Rd | 18 glmmTMB-1.0.0/glmmTMB/man/ranef.glmmTMB.Rd | 33 - glmmTMB-1.0.0/glmmTMB/man/sigma.glmmTMB.Rd | 36 - glmmTMB-1.0.0/glmmTMB/man/splitForm.Rd | 10 glmmTMB-1.0.0/glmmTMB/man/weights.glmmTMB.Rd |only glmmTMB-1.0.0/glmmTMB/src/Makevars.in |only glmmTMB-1.0.0/glmmTMB/src/glmmTMB.cpp | 59 + glmmTMB-1.0.0/glmmTMB/tests/testthat/test-VarCorr.R | 18 glmmTMB-1.0.0/glmmTMB/tests/testthat/test-bootMer.R |only glmmTMB-1.0.0/glmmTMB/tests/testthat/test-control.R | 34 + glmmTMB-1.0.0/glmmTMB/tests/testthat/test-disp.R | 16 glmmTMB-1.0.0/glmmTMB/tests/testthat/test-downstream.R | 57 + glmmTMB-1.0.0/glmmTMB/tests/testthat/test-families.R | 42 + glmmTMB-1.0.0/glmmTMB/tests/testthat/test-mapopt.R |only glmmTMB-1.0.0/glmmTMB/tests/testthat/test-methods.R | 68 -- glmmTMB-1.0.0/glmmTMB/tests/testthat/test-predict.R | 84 ++ glmmTMB-1.0.0/glmmTMB/tests/testthat/test-start.R |only glmmTMB-1.0.0/glmmTMB/tests/testthat/test-weight.R | 42 - glmmTMB-1.0.0/glmmTMB/tests/testthat/test-zi.R | 21 glmmTMB-1.0.0/glmmTMB/vignettes/covstruct.rmd | 46 - glmmTMB-1.0.0/glmmTMB/vignettes/glmmTMB.Rnw | 6 glmmTMB-1.0.0/glmmTMB/vignettes/model_evaluation.Rnw |only glmmTMB-1.0.0/glmmTMB/vignettes/parallel.Rmd |only glmmTMB-1.0.0/glmmTMB/vignettes/troubleshooting.rmd | 179 ++++- 92 files changed, 2326 insertions(+), 914 deletions(-)
Title: Generalized Hyperbolic Distribution and Its Special Cases
Description: Detailed functionality for working
with the univariate and multivariate Generalized Hyperbolic
distribution and its special cases (Hyperbolic (hyp), Normal
Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t
and Gaussian distribution). Especially, it contains fitting
procedures, an AIC-based model selection routine, and functions
for the computation of density, quantile, probability, random
variates, expected shortfall and some portfolio optimization
and plotting routines as well as the likelihood ratio test. In
addition, it contains the Generalized Inverse Gaussian
distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts.
Quantitative risk management: Concepts, techniques and tools.
Princeton University Press, Princeton (2005).
Author: David Luethi, Wolfgang Breymann
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between ghyp versions 1.5.8 dated 2020-01-23 and 1.5.9 dated 2020-02-03
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/Generalized_Hyperbolic_Distribution.pdf |binary man/transform-extract-methods.Rd | 1 - 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Powell Wheeler [aut],
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.26 dated 2019-11-22 and 0.8.27 dated 2020-02-03
DESCRIPTION | 13 MD5 | 204 ++++++------ NAMESPACE | 2 NEWS.md | 6 R/FSA-internals.R | 23 + R/FSAUtils.R | 16 - R/fitPlot.R | 2 R/lwCompPreds.R | 1 inst/helpers/installTester.R | 4 man/BluegillJL.Rd | 88 ++--- man/BrookTroutTH.Rd | 76 ++-- man/ChinookArg.Rd | 80 ++--- man/CodNorwegian.Rd | 82 ++--- man/CutthroatAL.Rd | 110 +++--- man/Ecoli.Rd | 62 +-- man/FSA-internals.Rd | 59 +-- man/FSA.Rd | 49 +-- man/FSAUtils.Rd | 96 +++--- man/Mirex.Rd | 84 ++--- man/PSDlit.Rd | 108 +++--- man/PikeNY.Rd | 90 ++--- man/PikeNYPartial1.Rd | 96 +++--- man/SMBassLS.Rd | 90 ++--- man/SMBassWB.Rd | 120 +++---- man/Schnute.Rd | 140 ++++---- man/SchnuteRichards.Rd | 103 +++--- man/SpotVA1.Rd | 80 ++--- man/Subset.Rd | 136 ++++---- man/Summarize.Rd | 224 +++++++------- man/WR79.Rd | 86 ++--- man/WSlit.Rd | 122 +++---- man/WhitefishLC.Rd | 100 +++--- man/addZeroCatch.Rd | 270 ++++++++--------- man/ageBias.Rd | 656 ++++++++++++++++++++++------------------- man/agePrecision.Rd | 312 ++++++++++--------- man/alkAgeDist.Rd | 150 ++++----- man/alkIndivAge.Rd | 246 +++++++-------- man/alkMeanVar.Rd | 167 +++++----- man/alkPlot.Rd | 215 +++++++------ man/binCI.Rd | 143 ++++----- man/bootCase.Rd | 266 +++++++++------- man/capHistConvert.Rd | 615 +++++++++++++++++++-------------------- man/capHistSum.Rd | 197 ++++++------ man/catchCurve.Rd | 359 ++++++++++++---------- man/chapmanRobson.Rd | 314 ++++++++++--------- man/chooseColors.Rd | 90 ++--- man/col2rgbt.Rd | 72 ++-- man/compIntercepts.Rd | 155 +++++---- man/compSlopes.Rd | 163 +++++----- man/depletion.Rd | 350 +++++++++++----------- man/diags.Rd | 139 ++++---- man/dunnTest.Rd | 230 +++++++------- man/expandCounts.Rd | 259 ++++++++-------- man/expandLenFreq.Rd | 164 +++++----- man/extraTests.Rd | 216 ++++++------- man/fact2num.Rd | 74 ++-- man/fishR.Rd | 67 ++-- man/fitPlot.Rd | 551 +++++++++++++++++++--------------- man/fsaNews.Rd | 56 +-- man/geomean.Rd | 108 +++--- man/growthModels.Rd | 678 +++++++++++++++++++++---------------------- man/headtail.Rd | 118 +++---- man/hist.formula.Rd | 290 +++++++++--------- man/histFromSum.Rd | 158 +++++----- man/hoCoef.Rd | 83 ++--- man/hyperCI.Rd | 74 ++-- man/knitUtil.Rd | 238 ++++++++------- man/ksTest.Rd | 136 ++++---- man/lagratio.Rd | 118 +++---- man/lencat.Rd | 427 ++++++++++++++------------- man/logbtcf.Rd | 106 +++--- man/lwCompPreds.Rd | 258 ++++++++-------- man/mapvalues.Rd | 14 man/metaM.Rd | 344 +++++++++++---------- man/mrClosed.Rd | 532 ++++++++++++++++++--------------- man/mrOpen.Rd | 316 ++++++++++---------- man/nlsBoot.Rd | 214 +++++++------ man/nlsTracePlot.Rd | 191 ++++++------ man/oddeven.Rd | 72 ++-- man/peek.Rd | 116 +++---- man/perc.Rd | 105 +++--- man/plotAB.Rd | 232 +++++++------- man/plotBinResp.Rd | 233 +++++++------- man/poiCI.Rd | 106 +++--- man/psdAdd.Rd | 240 ++++++++------- man/psdCI.Rd | 195 ++++++------ man/psdCalc.Rd | 246 ++++++++------- man/psdPlot.Rd | 286 +++++++++--------- man/psdVal.Rd | 151 ++++----- man/rSquared.Rd | 93 ++--- man/rcumsum.Rd | 142 ++++----- man/removal.Rd | 495 ++++++++++++++++--------------- man/repeatedRows2Keep.Rd | 88 ++--- man/residPlot.Rd | 521 ++++++++++++++++++--------------- man/se.Rd | 82 ++--- man/srStarts.Rd | 219 +++++++------ man/stockRecruitment.Rd | 262 ++++++++-------- man/sumTable.Rd | 127 +++----- man/tictactoe.Rd | 180 +++++------ man/validn.Rd | 88 ++--- man/vbStarts.Rd | 316 ++++++++++---------- man/wrAdd.Rd | 159 +++++----- man/wsVal.Rd | 122 +++---- 103 files changed, 9520 insertions(+), 8807 deletions(-)
Title: Estimate Entry Models
Description: Tools for measuring empirically the effects of entry in concentrated markets, based in Bresnahan and Reiss (1991) <https://www.jstor.org/stable/2937655>.
Author: Guilherme Jardim [aut, cre],
Arthur Bragança [ctb],
Pedro Fernandes [ctb]
Maintainer: Guilherme Jardim <gnjardim1@gmail.com>
Diff between entrymodels versions 0.1.0 dated 2019-11-25 and 0.2.0 dated 2020-02-03
DESCRIPTION | 6 +- MD5 | 13 +++--- NEWS.md |only R/em_2var.R | 19 ++++++--- R/em_basic.R | 12 +++-- README.md | 117 +++++++++++++++++++++++++++++++++----------------------- man/em_2var.Rd | 15 +++++-- man/em_basic.Rd | 3 - 8 files changed, 114 insertions(+), 71 deletions(-)
Title: Functions for Ecdat
Description: Functions to update data sets in Ecdat and to create,
manipulate, plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.2-0 dated 2019-02-25 and 0.2-2 dated 2020-02-03
Ecfun-0.2-0/Ecfun/R/read.testURLs.R |only Ecfun-0.2-0/Ecfun/R/testURLs.R |only Ecfun-0.2-0/Ecfun/man/read.testURLs.Rd |only Ecfun-0.2-0/Ecfun/man/testURLs.Rd |only Ecfun-0.2-2/Ecfun/DESCRIPTION | 24 Ecfun-0.2-2/Ecfun/MD5 | 105 - Ecfun-0.2-2/Ecfun/NAMESPACE | 20 Ecfun-0.2-2/Ecfun/NEWS.md |only Ecfun-0.2-2/Ecfun/R/BoxCox.R | 4 Ecfun-0.2-2/Ecfun/R/asNumericChar.R | 117 + Ecfun-0.2-2/Ecfun/R/asNumericDF.R | 179 -- Ecfun-0.2-2/Ecfun/R/simulate.bic.glm.R |only Ecfun-0.2-2/Ecfun/R/simulate.glm.R |only Ecfun-0.2-2/Ecfun/README.md |only Ecfun-0.2-2/Ecfun/build/vignette.rds |binary Ecfun-0.2-2/Ecfun/inst/doc/UpdatingUSGDPpresidents.R |only Ecfun-0.2-2/Ecfun/inst/doc/UpdatingUSGDPpresidents.Rmd |only Ecfun-0.2-2/Ecfun/inst/doc/UpdatingUSGDPpresidents.html |only Ecfun-0.2-2/Ecfun/inst/doc/nuclearArmageddon.R |only Ecfun-0.2-2/Ecfun/inst/doc/nuclearArmageddon.Rmd | 12 Ecfun-0.2-2/Ecfun/inst/doc/nuclearArmageddon.html | 233 +-- Ecfun-0.2-2/Ecfun/inst/doc/update_nuclearWeaponStates.R |only Ecfun-0.2-2/Ecfun/inst/doc/update_nuclearWeaponStates.Rmd |only Ecfun-0.2-2/Ecfun/inst/doc/update_nuclearWeaponStates.html |only Ecfun-0.2-2/Ecfun/man/BoxCox.Rd | 24 Ecfun-0.2-2/Ecfun/man/Dates3to1.Rd | 2 Ecfun-0.2-2/Ecfun/man/Interp.Rd | 24 Ecfun-0.2-2/Ecfun/man/USsenateClass.Rd | 14 Ecfun-0.2-2/Ecfun/man/asNumericDF.Rd | 291 ++- Ecfun-0.2-2/Ecfun/man/classIndex.Rd | 2 Ecfun-0.2-2/Ecfun/man/confint.var.Rd | 2 Ecfun-0.2-2/Ecfun/man/dateCols.Rd | 12 Ecfun-0.2-2/Ecfun/man/financialCrisisFiles.Rd | 57 Ecfun-0.2-2/Ecfun/man/grepNonStandardCharacters.Rd | 8 Ecfun-0.2-2/Ecfun/man/interpChar.Rd | 470 +++--- Ecfun-0.2-2/Ecfun/man/interpPairs.Rd | 993 ++++++------- Ecfun-0.2-2/Ecfun/man/logVarCor.Rd | 2 Ecfun-0.2-2/Ecfun/man/match.data.frame.Rd | 212 +- Ecfun-0.2-2/Ecfun/man/matchName.Rd | 472 +++--- Ecfun-0.2-2/Ecfun/man/matchQuote.Rd | 22 Ecfun-0.2-2/Ecfun/man/mergeUShouse.senate.Rd | 2 Ecfun-0.2-2/Ecfun/man/mergeVote.Rd | 259 +-- Ecfun-0.2-2/Ecfun/man/parseCommas.Rd | 166 +- Ecfun-0.2-2/Ecfun/man/parseName.Rd | 391 ++--- Ecfun-0.2-2/Ecfun/man/qqnorm2.Rd | 20 Ecfun-0.2-2/Ecfun/man/rasterImageAdj.Rd | 359 ++-- Ecfun-0.2-2/Ecfun/man/read.transpose.Rd | 30 Ecfun-0.2-2/Ecfun/man/readDates3to1.Rd | 11 Ecfun-0.2-2/Ecfun/man/readFinancialCrisisFiles.Rd | 52 Ecfun-0.2-2/Ecfun/man/readUSsenate.Rd | 2 Ecfun-0.2-2/Ecfun/man/recode2.Rd | 132 - Ecfun-0.2-2/Ecfun/man/simulate.bic.glm.Rd |only Ecfun-0.2-2/Ecfun/man/simulate.glm.Rd |only Ecfun-0.2-2/Ecfun/man/strsplit1.Rd | 7 Ecfun-0.2-2/Ecfun/man/subNonStandardCharacters.Rd | 15 Ecfun-0.2-2/Ecfun/man/subNonStandardNames.Rd | 36 Ecfun-0.2-2/Ecfun/man/trimImage.Rd | 324 ++-- Ecfun-0.2-2/Ecfun/man/truncdist.Rd | 9 Ecfun-0.2-2/Ecfun/vignettes/UpdatingUSGDPpresidents.Rmd |only Ecfun-0.2-2/Ecfun/vignettes/nuc-references.bib |only Ecfun-0.2-2/Ecfun/vignettes/nuclearArmageddon.Rmd | 12 Ecfun-0.2-2/Ecfun/vignettes/nuclearProliferation.svg |only Ecfun-0.2-2/Ecfun/vignettes/nuclearWeaponStates.html |only Ecfun-0.2-2/Ecfun/vignettes/time2Armgeddon.svg |only Ecfun-0.2-2/Ecfun/vignettes/update_nuclearWeaponStates.Rmd |only 65 files changed, 2730 insertions(+), 2398 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6-3 dated 2019-10-23 and 4.6-4.1 dated 2020-02-03
doBy-4.6-3/doBy/R/data-doBy.R |only doBy-4.6-3/doBy/man/data-NIRmilk.Rd |only doBy-4.6-3/doBy/man/data-beets.Rd |only doBy-4.6-3/doBy/man/data-breastcancer.Rd |only doBy-4.6-3/doBy/man/data-budworm.Rd |only doBy-4.6-3/doBy/man/data-carcass.Rd |only doBy-4.6-3/doBy/man/data-codstom.Rd |only doBy-4.6-3/doBy/man/data-crimeRate.Rd |only doBy-4.6-3/doBy/man/data-dietox.Rd |only doBy-4.6-3/doBy/man/data-haldCement.Rd |only doBy-4.6-3/doBy/man/data-milkman.Rd |only doBy-4.6-3/doBy/man/data-potatoes.Rd |only doBy-4.6-4.1/doBy/ChangeLog | 7 doBy-4.6-4.1/doBy/DESCRIPTION | 12 - doBy-4.6-4.1/doBy/MD5 | 116 +++++----- doBy-4.6-4.1/doBy/NAMESPACE | 279 ++++++++++++-------------- doBy-4.6-4.1/doBy/NEWS |only doBy-4.6-4.1/doBy/R/BY-lapplyBy.R | 9 doBy-4.6-4.1/doBy/R/BY-lmBy.R | 60 +++-- doBy-4.6-4.1/doBy/R/BY-orderBy.R | 7 doBy-4.6-4.1/doBy/R/BY-sampleBy.R | 13 - doBy-4.6-4.1/doBy/R/BY-splitBy2.R | 158 +++++++------- doBy-4.6-4.1/doBy/R/BY-subsetBy.R | 31 +- doBy-4.6-4.1/doBy/R/BY-summaryBy2.R | 213 +++++++++---------- doBy-4.6-4.1/doBy/R/BY-transformBy.R | 8 doBy-4.6-4.1/doBy/R/data-doby.R |only doBy-4.6-4.1/doBy/R/descStat.R | 9 doBy-4.6-4.1/doBy/R/doby-utilities.R | 19 - doBy-4.6-4.1/doBy/R/dobyxtabs.R | 2 doBy-4.6-4.1/doBy/R/esticon.R | 71 +++--- doBy-4.6-4.1/doBy/R/firstlastObs.R | 16 - doBy-4.6-4.1/doBy/R/linest_LSmeans.R | 10 doBy-4.6-4.1/doBy/R/linest_compute.R | 13 + doBy-4.6-4.1/doBy/R/linest_get.R | 14 + doBy-4.6-4.1/doBy/R/linest_matrix.R | 6 doBy-4.6-4.1/doBy/R/linest_utilities.R | 6 doBy-4.6-4.1/doBy/R/namespace.R |only doBy-4.6-4.1/doBy/R/specialize.R | 1 doBy-4.6-4.1/doBy/R/taylor.R | 1 doBy-4.6-4.1/doBy/R/which.maxn.R | 1 doBy-4.6-4.1/doBy/build/vignette.rds |binary doBy-4.6-4.1/doBy/data/cropyield.RData |only doBy-4.6-4.1/doBy/data/datalist | 1 doBy-4.6-4.1/doBy/data/fev.rda |binary doBy-4.6-4.1/doBy/inst/doc/doby.R | 10 doBy-4.6-4.1/doBy/inst/doc/doby.pdf |binary doBy-4.6-4.1/doBy/inst/doc/linest-lsmeans.R | 4 doBy-4.6-4.1/doBy/inst/doc/linest-lsmeans.pdf |binary doBy-4.6-4.1/doBy/man/NIRmilk.Rd |only doBy-4.6-4.1/doBy/man/beets.Rd |only doBy-4.6-4.1/doBy/man/breastcancer.Rd |only doBy-4.6-4.1/doBy/man/budworm.Rd |only doBy-4.6-4.1/doBy/man/by-lmby.Rd | 26 +- doBy-4.6-4.1/doBy/man/by-sample.Rd | 14 - doBy-4.6-4.1/doBy/man/by-split.Rd | 9 doBy-4.6-4.1/doBy/man/by-subset.Rd | 35 ++- doBy-4.6-4.1/doBy/man/by-summary.Rd | 20 + doBy-4.6-4.1/doBy/man/carcass.Rd |only doBy-4.6-4.1/doBy/man/codstom.Rd |only doBy-4.6-4.1/doBy/man/crimeRate.Rd |only doBy-4.6-4.1/doBy/man/cropyield.Rd |only doBy-4.6-4.1/doBy/man/descStat.Rd | 4 doBy-4.6-4.1/doBy/man/dietox.Rd |only doBy-4.6-4.1/doBy/man/esticon.Rd | 33 +-- doBy-4.6-4.1/doBy/man/fatacid.Rd | 2 doBy-4.6-4.1/doBy/man/fev.Rd | 8 doBy-4.6-4.1/doBy/man/firstlastobs.Rd | 5 doBy-4.6-4.1/doBy/man/haldCement.Rd |only doBy-4.6-4.1/doBy/man/linest-matrix.Rd | 2 doBy-4.6-4.1/doBy/man/linest.Rd | 3 doBy-4.6-4.1/doBy/man/ls-means.Rd | 12 - doBy-4.6-4.1/doBy/man/milkman.Rd |only doBy-4.6-4.1/doBy/man/potatoes.Rd |only 73 files changed, 659 insertions(+), 611 deletions(-)
Title: Dave Armstrong's Miscellaneous Functions
Description: Miscellaneous set of functions I use in my teaching either at the University of Western Ontario or the Inter-university Consortium for Political and Social Research (ICPSR) Summer Program in Quantitative Methods. Broadly, the functions help with presentation and interpretation of LMs and GLMs, but also implement some new tools like Alternating Least Squares Optimal Scaling for dependent variables, a Bayesian analog to the ALSOS algorithm. There are also tools to help understand interactions in both LMs and binary GLMs.
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <dave@quantoid.net>
Diff between DAMisc versions 1.5 dated 2019-06-25 and 1.5.1 dated 2020-02-03
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 - R/DAMisc_functions.R | 25 ++++++++++++++++--------- README.md | 5 +++++ man/crSpanTest.Rd | 1 - 6 files changed, 32 insertions(+), 22 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.2-2 dated 2019-11-05 and 1.2-3 dated 2020-02-03
DESCRIPTION | 10 ++-- MD5 | 16 +++---- NAMESPACE | 1 R/baseline.als.R | 67 +++++++++++++++++++++++++++++ R/baseline.fillPeaks.R | 104 ++++++++++++++++++++++++++++++++++++++++++++-- R/baseline.irls.R | 65 ++++++++++++++++++++++++++++ R/baseline.lowpass.R | 2 R/baseline.medianWindow.R | 2 R/baseline.modpolyfit.R | 2 9 files changed, 250 insertions(+), 19 deletions(-)
Title: Estimation and Prediction for Remote Effects Spatial Process
Models
Description: Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@duke.edu>
Diff between telefit versions 1.0.2 dated 2019-12-17 and 1.0.3 dated 2020-02-03
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 3 --- NEWS.md | 5 +++-- R/extractRegion.R | 37 ++++++++++++++++++------------------- R/stPredict.R | 3 +-- 6 files changed, 34 insertions(+), 38 deletions(-)
Title: Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Description: Helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich <https://fgcz.ch>. We use this package
mainly for prototyping, teaching, and having fun with proteomics data.
But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>),
Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>),
Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
Diff between protViz versions 0.5.1 dated 2019-11-18 and 0.6.0 dated 2020-02-03
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- README.md | 7 ++++++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/PTM_MarkerFinder.R | 1 - inst/doc/PTM_MarkerFinder.pdf |binary inst/doc/poster.R | 1 - inst/doc/poster.pdf |binary inst/doc/protViz.R | 1 - inst/doc/protViz.pdf |binary man/PTM_MarkerFinder.Rd | 2 -- src/RcppExports.cpp | 1 - 14 files changed, 29 insertions(+), 23 deletions(-)
Title: Multi-Objective Kriging Optimization
Description: Multi-Objective optimization based on the Kriging metamodel.
Important functions: mkm() (builder for the multiobjective models), MVPF() (sequential minimizator using variance reduction),
MEGO() (generalization of ParEgo) and HEGO() (minimizator using the expected hypervolume improvement).
References are Passos and Luersen (2018) <doi:10.1590/1679-78254324>.
Author: Adriano Passos [aut, cre],
Marco Luersen [ctb]
Maintainer: Adriano Passos <adriano.utfpr@gmail.com>
Diff between moko versions 1.0.1 dated 2017-07-08 and 1.0.2 dated 2020-02-03
moko-1.0.1/moko/man/VMPF.Rd |only moko-1.0.2/moko/DESCRIPTION | 12 moko-1.0.2/moko/MD5 | 57 +-- moko-1.0.2/moko/NAMESPACE | 3 moko-1.0.2/moko/R/moko.R | 2 moko-1.0.2/moko/R/optim_hego.R | 6 moko-1.0.2/moko/R/optim_vmpf.R | 26 + moko-1.0.2/moko/R/ps_metrics.R | 2 moko-1.0.2/moko/build/vignette.rds |binary moko-1.0.2/moko/inst/doc/nb_vignette.R | 28 - moko-1.0.2/moko/inst/doc/nb_vignette.html | 536 ++++++++++++++++++++---------- moko-1.0.2/moko/man/EHVI.Rd | 138 +++---- moko-1.0.2/moko/man/EI.Rd | 132 +++---- moko-1.0.2/moko/man/HEGO.Rd | 158 ++++---- moko-1.0.2/moko/man/MEGO.Rd | 328 +++++++++--------- moko-1.0.2/moko/man/MVPF.Rd |only moko-1.0.2/moko/man/Tchebycheff.Rd | 80 ++-- moko-1.0.2/moko/man/igd.Rd | 86 ++-- moko-1.0.2/moko/man/max_EHVI.Rd | 135 +++---- moko-1.0.2/moko/man/max_EI.Rd | 131 +++---- moko-1.0.2/moko/man/mkm-class.Rd | 88 ++-- moko-1.0.2/moko/man/mkm.Rd | 108 +++--- moko-1.0.2/moko/man/moko.Rd | 27 - moko-1.0.2/moko/man/nowacki_beam.Rd | 109 +++--- moko-1.0.2/moko/man/nowacki_beam_tps.Rd | 26 - moko-1.0.2/moko/man/package-deprecated.Rd |only moko-1.0.2/moko/man/pdist.Rd | 46 +- moko-1.0.2/moko/man/predict-mkm-method.Rd | 81 ++-- moko-1.0.2/moko/man/predict_front.Rd | 98 ++--- moko-1.0.2/moko/man/ps.Rd | 56 +-- moko-1.0.2/moko/man/test_functions.Rd | 112 +++--- 31 files changed, 1442 insertions(+), 1169 deletions(-)
Title: A Multiscale Test of Spatial Stationarity for LS2W Processes
Description: Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.
Author: Sarah Taylor [aut],
Matt Nunes [aut, cre],
Idris Eckley [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between LS2Wstat versions 2.1-1 dated 2018-07-18 and 2.1-2 dated 2020-02-03
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- R/simTexture.R | 20 ++++++++++---------- man/simTexture.Rd | 8 ++++---- 5 files changed, 24 insertions(+), 24 deletions(-)
Title: Two-Step Kernel Ridge Regression for Network Predictions
Description: Fit a two-step kernel ridge regression model for
predicting edges in networks, and carry out cross-validation
using shortcuts for swift and accurate performance assessment
(Stock et al, 2018 <doi:10.1093/bib/bby095> ).
Author: Joris Meys [cre, aut],
Michiel Stock [aut]
Maintainer: Joris Meys <Joris.Meys@UGent.be>
Diff between xnet versions 0.1.10 dated 2020-01-09 and 0.1.11 dated 2020-02-03
DESCRIPTION | 10 MD5 | 122 ++++---- NAMESPACE | 2 NEWS.md | 7 R/getters_tskrrImpute.R | 1 R/getters_tskrrTune.R | 1 R/linear_filter.R | 8 R/weights.R | 1 build/vignette.rds |binary inst/doc/Preparation_example_data.html | 12 inst/doc/xnet_ClassStructure.html | 12 inst/doc/xnet_ShortIntroduction.html | 12 man/as_tuned.Rd | 134 ++++----- man/create_grid.Rd | 80 ++--- man/dim-tskrr-method.Rd | 58 +-- man/drugTargetInteraction.Rd | 90 +++--- man/eigen2hat.Rd | 94 +++--- man/fitted.Rd | 90 +++--- man/get_loo_fun.Rd | 190 ++++++------- man/getters-permtest.Rd | 82 ++--- man/getters-tskrr.Rd | 194 ++++++------- man/getters-tskrrImpute.Rd | 110 +++---- man/getters-tskrrTune.Rd | 130 ++++---- man/getters_linearFilter.Rd | 122 ++++---- man/hat.Rd | 64 ++-- man/impute_tskrr.Rd | 168 +++++------ man/impute_tskrr.fit.Rd | 154 +++++----- man/is_symmetric.Rd | 62 ++-- man/labels.Rd | 140 ++++----- man/linearFilter-class.Rd | 68 ++-- man/linear_filter.Rd | 74 ++--- man/loo.Rd | 160 +++++----- man/looInternal.Rd | 144 ++++----- man/loss.Rd | 166 +++++------ man/loss_functions.Rd | 104 +++---- man/match_labels.Rd | 80 ++--- man/permtest-class.Rd | 98 +++--- man/permtest.Rd | 196 ++++++------- man/plot.tskrr.Rd | 256 ++++++++--------- man/plot_grid.Rd | 146 +++++----- man/predict.Rd | 234 ++++++++-------- man/proteinInteraction.Rd | 78 ++--- man/residuals.tskrr.Rd | 162 +++++------ man/test_symmetry.Rd | 72 ++-- man/tskrr-class.Rd | 72 ++-- man/tskrr.Rd | 162 +++++------ man/tskrr.fit.Rd | 124 ++++---- man/tskrrHeterogeneous-class.Rd | 80 ++--- man/tskrrHomogeneous-class.Rd | 78 ++--- man/tskrrImpute-class.Rd | 48 +-- man/tskrrImputeHeterogeneous-class.Rd | 98 +++--- man/tskrrImputeHomogeneous-class.Rd | 98 +++--- man/tskrrTune-class.Rd | 94 +++--- man/tskrrTuneHeterogeneous-class.Rd | 26 - man/tskrrTuneHomogeneous-class.Rd | 26 - man/tune.Rd | 350 ++++++++++++------------ man/update.Rd | 118 ++++---- man/valid_dimensions.Rd | 68 ++-- man/valid_labels.Rd | 94 +++--- man/weights.Rd | 64 ++-- man/xnet-package.Rd | 48 +-- tests/testthat/test_linearFilter_calculations.R | 4 62 files changed, 2919 insertions(+), 2921 deletions(-)
Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using
the methods of Fasiolo et al. (2017) <arXiv:1707.03307>. Differently from
'quantreg', the smoothing parameters are estimated automatically by marginal
loss minimization, while the regression coefficients are estimated using either
PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian
credible intervals of the estimated effects have approximately the correct
coverage. The main function is qgam() which is similar to gam() in 'mgcv', but
fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre],
Simon N. Wood [ctb],
Margaux Zaffran [ctb],
Yannig Goude [ctb],
Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between qgam versions 1.3.1 dated 2020-02-01 and 1.3.2 dated 2020-02-03
DESCRIPTION | 8 +++--- MD5 | 24 ++++++++++---------- R/I_getErrParam.R | 2 - R/qgam.R | 1 build/vignette.rds |binary inst/doc/qgam.R | 60 +++++++++++++++++++++++++-------------------------- inst/doc/qgam.html | 52 ++++++++++++++++++++++---------------------- man/cqcheck.Rd | 13 +++++++++-- man/cqcheckI.Rd | 11 +++++++-- man/mqgam.Rd | 17 +++++++++++--- man/qgam.Rd | 19 +++++++++++----- man/tuneLearn.Rd | 17 +++++++++++--- man/tuneLearnFast.Rd | 16 ++++++++++--- 13 files changed, 144 insertions(+), 96 deletions(-)
Title: Bayesian Non-Parametric Latent-Class Capture-Recapture
Description: Bayesian population size estimation using non parametric latent-class models.
Author: Daniel Manrique-Vallier
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>
Diff between LCMCR versions 0.4.3 dated 2017-07-08 and 0.4.11 dated 2020-02-03
LCMCR-0.4.11/LCMCR/DESCRIPTION | 10 LCMCR-0.4.11/LCMCR/MD5 | 78 ++-- LCMCR-0.4.11/LCMCR/R/ArrayUtils.R |only LCMCR-0.4.11/LCMCR/R/CR_Support.R |only LCMCR-0.4.11/LCMCR/R/Lcm_CR_Strat_fn.R |only LCMCR-0.4.11/LCMCR/R/Lcm_CR_fn.R |only LCMCR-0.4.11/LCMCR/R/MCMCenv_refClass.R |only LCMCR-0.4.11/LCMCR/data/kosovo_aggregate.RData |binary LCMCR-0.4.11/LCMCR/man/LCMCR-package.Rd | 17 - LCMCR-0.4.11/LCMCR/man/lcmCR.Rd | 2 LCMCR-0.4.11/LCMCR/man/lcmCR_PostSampl.Rd | 2 LCMCR-0.4.11/LCMCR/src/CData_DM.h | 7 LCMCR-0.4.11/LCMCR/src/CData_DM_Strat.h |only LCMCR-0.4.11/LCMCR/src/Makevars | 13 LCMCR-0.4.11/LCMCR/src/NPLCM_CR_Basic_Freq.cpp | 156 +++++---- LCMCR-0.4.11/LCMCR/src/NPLCM_CR_Basic_Freq.h | 23 - LCMCR-0.4.11/LCMCR/src/NPLCM_CR_Strat_Freq.cpp |only LCMCR-0.4.11/LCMCR/src/NPLCM_CR_Strat_Freq.h |only LCMCR-0.4.11/LCMCR/src/R_Interface |only LCMCR-0.4.11/LCMCR/src/daniel2/CChain.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CChain.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CData.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CData.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CPar_Data_Type.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CParam.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CParam.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CParam_generic.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CParams_generic.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CVariable_Container.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/CVariable_Container.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/Model_Environ.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/R_Environ_Simple.cpp | 276 ++++++++--------- LCMCR-0.4.11/LCMCR/src/daniel2/R_Environ_Simple.h | 12 LCMCR-0.4.11/LCMCR/src/daniel2/dan_array_utils.cpp | 2 LCMCR-0.4.11/LCMCR/src/daniel2/dan_array_utils.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/dan_math.h | 2 LCMCR-0.4.11/LCMCR/src/daniel2/dan_math_gsl.h | 3 LCMCR-0.4.11/LCMCR/src/daniel2/dan_sys.h | 2 LCMCR-0.4.11/LCMCR/src/definitions.h | 2 LCMCR-0.4.3/LCMCR/R/Rcode.R |only LCMCR-0.4.3/LCMCR/src/CData_DM.cpp |only LCMCR-0.4.3/LCMCR/src/Makevars.win |only LCMCR-0.4.3/LCMCR/src/R_Lcm_CR.cpp |only LCMCR-0.4.3/LCMCR/src/R_Lcm_CR.h |only LCMCR-0.4.3/LCMCR/src/registration.cpp |only 45 files changed, 333 insertions(+), 300 deletions(-)
Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions
from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>.
'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates
the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are
also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre],
Michael Krabbe Borregaard [aut],
Karl Ugland [aut],
Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>
Diff between gambin versions 2.4.1 dated 2019-03-03 and 2.4.3 dated 2020-02-03
DESCRIPTION | 8 - MD5 | 40 +++---- NAMESPACE | 2 NEWS.md | 4 R/fit_gambin.R | 1 build/vignette.rds |binary inst/doc/overview.R | 2 inst/doc/overview.html | 30 +++-- man/categ.Rd | 42 +++---- man/create_octaves.Rd | 60 +++++----- man/deconstruct_modes.Rd | 193 ++++++++++++++++++----------------- man/dgambin.Rd | 178 ++++++++++++++++---------------- man/fit_abundances.Rd | 135 +++++++++++------------- man/fly.Rd | 42 +++---- man/gambin-package.Rd | 98 ++++++++--------- man/logLik.gambin.Rd | 82 +++++++------- man/moths.Rd | 30 ++--- man/mult_abundances.Rd | 142 ++++++++++++------------- man/summary.gambin.Rd | 120 ++++++++++----------- tests/testthat.R | 4 tests/testthat/test_fitAbundances.R |only tests/testthat/test_multAbundances.R |only 22 files changed, 615 insertions(+), 598 deletions(-)
Title: Double Generalized Linear Models Extending Poisson Regression
Description: Model estimation, dispersion testing and diagnosis of hyper-Poisson
Saez-Castillo, A.J. and Conde-Sanchez, A. (2013)
<doi:10.1016/j.csda.2012.12.009> and Conway-Maxwell-Poisson Huang, A. (2017)
<doi:10.1177/1471082X17697749> regression models.
Author: Antonio Jose Saez-Castillo [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between DGLMExtPois versions 0.1.0 dated 2019-08-01 and 0.1.1 dated 2020-02-03
DESCRIPTION | 10 - MD5 | 44 ++-- NAMESPACE | 2 NEWS.md | 8 R/marginal-probabilities-and-expectations.R | 2 README.md | 5 man/AIC.Rd | 66 +++--- man/AIC_CMP.Rd | 66 +++--- man/Bids.Rd | 58 ++--- man/DGLMExtPois.Rd | 19 - man/confint.glm_CMP.Rd | 70 +++---- man/confint.glm_hP.Rd | 70 +++---- man/expected.Rd | 128 ++++++------- man/glm.CMP.Rd | 239 +++++++++++++----------- man/glm.hP.Rd | 273 ++++++++++++++-------------- man/hP.Rd | 102 +++++----- man/lrtest.Rd | 86 ++++---- man/plots.Rd | 102 +++++----- man/predict.glm_CMP.Rd | 67 +++--- man/predict.glm_hP.Rd | 69 +++---- man/residuals.Rd | 182 +++++++++--------- man/summary.glm_CMP.Rd | 78 ++++---- man/summary.glm_hP.Rd | 78 ++++---- 23 files changed, 938 insertions(+), 886 deletions(-)
Title: Contextualization and Evaluation of COI-5P Barcode Data
Description: Designed for the cleaning, contextualization and assessment of cytochrome c
oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains
functions for placing COI-5P barcode sequences into a common reading frame,
translating DNA sequences to amino acids and for assessing the likelihood that a
given barcode sequence includes an insertion or deletion error. The error assessment
relies on the comparison of input sequences against nucleotide and amino acid profile
hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713)
trained on a taxonomically diverse set of reference sequences. The functions are
provided as a complete pipeline and are also available individually for efficient and
targeted analysis of barcode data.
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <nugentc@uoguelph.ca>
Diff between coil versions 1.1.0 dated 2019-12-05 and 1.2.1 dated 2020-02-03
coil-1.1.0/coil/man/aa_PHMM.Rd |only coil-1.1.0/coil/man/nt_PHMM.Rd |only coil-1.2.1/coil/DESCRIPTION | 22 +-- coil-1.2.1/coil/MD5 | 49 +++---- coil-1.2.1/coil/R/coi5p.r | 45 ++++-- coil-1.2.1/coil/R/coil.r | 2 coil-1.2.1/coil/R/datasets.r | 10 - coil-1.2.1/coil/R/pipeline.r | 20 ++ coil-1.2.1/coil/R/subset_PHMM.r |only coil-1.2.1/coil/R/sysdata.rda |binary coil-1.2.1/coil/R/translation.r | 21 +-- coil-1.2.1/coil/README.md | 6 coil-1.2.1/coil/inst/doc/coil-vignette.R | 70 +++++++++- coil-1.2.1/coil/inst/doc/coil-vignette.Rmd | 117 ++++++++++++++--- coil-1.2.1/coil/inst/doc/coil-vignette.html | 157 ++++++++++++++++++++--- coil-1.2.1/coil/man/aa_coi_PHMM.Rd |only coil-1.2.1/coil/man/censored_translation.Rd | 6 coil-1.2.1/coil/man/coi5p.Rd | 3 coil-1.2.1/coil/man/coi5p_pipe.Rd | 19 ++ coil-1.2.1/coil/man/coil.Rd | 8 + coil-1.2.1/coil/man/frame.Rd | 20 +- coil-1.2.1/coil/man/indel_check.Rd | 14 +- coil-1.2.1/coil/man/nt_coi_PHMM.Rd |only coil-1.2.1/coil/man/subsetPHMM.Rd |only coil-1.2.1/coil/man/translate.Rd | 6 coil-1.2.1/coil/man/which_trans_table.Rd | 10 - coil-1.2.1/coil/tests/testthat/test_subsetPHMM.r |only coil-1.2.1/coil/tests/testthat/test_translate.r | 6 coil-1.2.1/coil/vignettes/coil-vignette.Rmd | 117 ++++++++++++++--- 29 files changed, 576 insertions(+), 152 deletions(-)
Title: Home Range Estimation
Description: A collection of tools for the estimation of animals home range.
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@ofb.gouv.fr>
Diff between adehabitatHR versions 0.4.16 dated 2019-04-07 and 0.4.18 dated 2020-02-03
adehabitatHR-0.4.16/adehabitatHR/build |only adehabitatHR-0.4.16/adehabitatHR/inst/doc/adehabitatHR.R |only adehabitatHR-0.4.16/adehabitatHR/inst/doc/adehabitatHR.Rnw |only adehabitatHR-0.4.18/adehabitatHR/DESCRIPTION | 10 +-- adehabitatHR-0.4.18/adehabitatHR/MD5 | 37 +++++------- adehabitatHR-0.4.18/adehabitatHR/R/kernelbb.r | 40 ++++++++++++- adehabitatHR-0.4.18/adehabitatHR/inst/doc/adehabitatHR.pdf |binary adehabitatHR-0.4.18/adehabitatHR/man/BRB.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/CharHull.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/LoCoH.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/MCHu.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/clusthr.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/estUD-class.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/findmax.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/getverticeshr.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/kernelUD.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/kernelbb.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/kernelkc.Rd | 4 - adehabitatHR-0.4.18/adehabitatHR/man/kerneloverlap.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/kver2spol.Rd | 2 adehabitatHR-0.4.18/adehabitatHR/man/mcp.Rd | 2 21 files changed, 75 insertions(+), 42 deletions(-)
Title: Simulation-Based Random Variable Objects
Description: Implements a simulation-based random variable class and a suite of
methods for extracting parts of random vectors, calculating extremes of random
vectors, and generating random vectors under a variety of distributions
following Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>.
Author: Jouni Kerman [aut],
Joseph Stachelek [ctb, cre]
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between rv versions 2.3.3 dated 2019-01-08 and 2.3.4 dated 2020-02-03
DESCRIPTION | 8 MD5 | 40 ++-- NEWS.md | 3 R/rv.R | 1 R/rvmatrix_rvarray.R | 1 build/vignette.rds |binary inst/doc/rv-doc.R | 70 ++++---- inst/doc/rv-doc.html | 409 +++++++++++++++++++++++++-------------------------- man/Extract-rv.Rd | 4 man/distrib_rv.Rd | 8 man/hist.rv.Rd | 10 - man/ivplot.Rd | 26 ++- man/matmult.Rd | 2 man/mlplot.Rd | 27 ++- man/points.rv.Rd | 19 +- man/rv.Rd | 2 man/rvarray.Rd | 5 man/rvmapply.Rd | 10 - man/rvquantile.Rd | 10 - man/splitbyname.Rd | 2 man/summaries.Rd | 3 21 files changed, 357 insertions(+), 303 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.2.1 dated 2019-05-26 and 2.2.2 dated 2020-02-03
DESCRIPTION | 16 +-- MD5 | 30 +++--- NEWS.md | 7 + R/lookfor.R | 7 - R/to_na.R | 1 README.md | 2 build/vignette.rds |binary inst/doc/intro_labelled.R | 74 +++++++------- inst/doc/intro_labelled.html | 215 +++++++++++++++++++++---------------------- man/labelled_spss.Rd | 3 man/look_for.Rd | 6 - man/recode.haven_labelled.Rd | 3 man/sort_val_labels.Rd | 9 - man/to_character.Rd | 8 + man/to_factor.Rd | 32 ++++-- man/val_labels_to_na.Rd | 2 16 files changed, 212 insertions(+), 203 deletions(-)
Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with link to associate outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 1.3.8 dated 2020-01-07 and 1.3.9 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/Umpire.pdf |binary man/e08-transforms.Rd | 2 -- 4 files changed, 7 insertions(+), 9 deletions(-)
Title: Multidimensional Penalized Splines for Survival and Net Survival
Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for
multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics.
See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 1.2.0 dated 2019-08-29 and 1.3.0 dated 2020-02-03
survPen-1.2.0/survPen/R/survPenV1_2.r |only survPen-1.2.0/survPen/tests/compar_LAML_LCV.pdf |only survPen-1.2.0/survPen/tests/compar_several_mods.pdf |only survPen-1.2.0/survPen/tests/compar_tensor_tint.pdf |only survPen-1.2.0/survPen/tests/compar_total_excess.pdf |only survPen-1.2.0/survPen/tests/compar_total_excess_CI.pdf |only survPen-1.2.0/survPen/tests/compar_unpen_pen.pdf |only survPen-1.2.0/survPen/tests/output_tests_survPen.lis |only survPen-1.2.0/survPen/tests/test_survPen.r |only survPen-1.3.0/survPen/DESCRIPTION | 11 survPen-1.3.0/survPen/MD5 | 86 ++--- survPen-1.3.0/survPen/NAMESPACE | 4 survPen-1.3.0/survPen/NEWS | 11 survPen-1.3.0/survPen/R/RcppExports.R |only survPen-1.3.0/survPen/R/survPenV1_30.r |only survPen-1.3.0/survPen/build/vignette.rds |binary survPen-1.3.0/survPen/inst/CITATION | 42 +- survPen-1.3.0/survPen/inst/doc/survival_analysis_with_survPen.Rmd | 2 survPen-1.3.0/survPen/inst/doc/survival_analysis_with_survPen.html | 167 +++++----- survPen-1.3.0/survPen/man/NR.beta.Rd | 4 survPen-1.3.0/survPen/man/NR.rho.Rd | 4 survPen-1.3.0/survPen/man/constraint.Rd | 2 survPen-1.3.0/survPen/man/cor.var.Rd | 2 survPen-1.3.0/survPen/man/crs.FP.Rd | 2 survPen-1.3.0/survPen/man/crs.Rd | 2 survPen-1.3.0/survPen/man/datCancer.Rd | 2 survPen-1.3.0/survPen/man/design.matrix.Rd | 4 survPen-1.3.0/survPen/man/grapes-mult-grapes.Rd |only survPen-1.3.0/survPen/man/grapes-vec-grapes.Rd |only survPen-1.3.0/survPen/man/instr.Rd | 2 survPen-1.3.0/survPen/man/inv.repam.Rd | 2 survPen-1.3.0/survPen/man/model.cons.Rd | 9 survPen-1.3.0/survPen/man/predict.survPen.Rd | 2 survPen-1.3.0/survPen/man/print.summary.survPen.Rd | 2 survPen-1.3.0/survPen/man/rd.Rd | 2 survPen-1.3.0/survPen/man/repam.Rd | 4 survPen-1.3.0/survPen/man/smf.Rd | 2 survPen-1.3.0/survPen/man/smooth.cons.Rd | 2 survPen-1.3.0/survPen/man/smooth.cons.integral.Rd | 2 survPen-1.3.0/survPen/man/smooth.spec.Rd | 6 survPen-1.3.0/survPen/man/summary.survPen.Rd | 2 survPen-1.3.0/survPen/man/survPen.Rd | 18 - survPen-1.3.0/survPen/man/survPen.fit.Rd | 4 survPen-1.3.0/survPen/man/survPenObject.Rd | 2 survPen-1.3.0/survPen/man/tensor.in.Rd | 2 survPen-1.3.0/survPen/man/tensor.prod.S.Rd | 2 survPen-1.3.0/survPen/man/tensor.prod.X.Rd | 2 survPen-1.3.0/survPen/src |only survPen-1.3.0/survPen/tests/testthat/test_Newton.R | 2 survPen-1.3.0/survPen/vignettes/survival_analysis_with_survPen.Rmd | 2 50 files changed, 217 insertions(+), 199 deletions(-)
Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis,
and sparse canonical correlation analysis, described in
Witten, Tibshirani and Hastie (2009)
<doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani
(2009) Extensions of sparse canonical correlation analysis,
with applications to genomic data
<doi:10.2202/1544-6115.1470>.
Author: Daniela Witten and Rob Tibshirani
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between PMA versions 1.2 dated 2020-01-16 and 1.2.1 dated 2020-02-03
PMA-1.2.1/PMA/DESCRIPTION | 8 ++++---- PMA-1.2.1/PMA/MD5 | 20 +++++++++----------- PMA-1.2.1/PMA/R/PMA-package.R | 1 + PMA-1.2.1/PMA/R/PMD.R | 1 - PMA-1.2.1/PMA/build/partial.rdb |binary PMA-1.2.1/PMA/man/CCA.Rd | 2 ++ PMA-1.2.1/PMA/man/PMD.Rd | 3 ++- PMA-1.2.1/PMA/man/PlotCGH.Rd | 3 ++- PMA-1.2.1/PMA/man/SPC.cv.Rd | 1 - PMA-1.2.1/PMA/man/breastdata.Rd | 6 ++++++ PMA-1.2/PMA/data |only 11 files changed, 26 insertions(+), 19 deletions(-)
Title: Fit Probabilistic Index Models
Description: Fit a probabilistic index model as described in
Thas et al, 2012: <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the
modeling function has changed in this new version. The old version is
still available at R-Forge.
Author: Joris Meys [aut, cre],
Jan De Neve [aut],
Nick Sabbe [aut],
Gustavo Guimaraes de Castro Amorim [aut]
Maintainer: Joris Meys <Joris.Meys@UGent.be>
Diff between pim versions 2.0.1 dated 2017-04-29 and 2.0.2 dated 2020-02-03
DESCRIPTION | 32 +-- MD5 | 136 ++++++++-------- NAMESPACE | 2 R/Estimators.R | 91 +++++------ R/LR.R | 30 +-- R/MHData.R | 2 R/SUData.R | 2 R/nobs.R | 25 +-- R/pim-package.R | 9 - R/pim.R | 127 +++++++-------- R/pim.fit.R | 38 ++-- R/print.R | 63 +++---- R/vcov.R | 18 +- R/zzz.R | 4 build/vignette.rds |binary data/DysData.rda |binary data/EngelData.rda |binary data/FEVData.rda |binary data/MHData.rda |binary data/SUData.rda |binary inst/doc/pim.R | 309 ++++++++++++++++++------------------- inst/doc/pim.pdf |binary man/CreateScoreFun.Rd | 60 +++---- man/DysData.Rd | 42 ++--- man/EngelData.Rd | 34 ++-- man/Extract.pim.summary.Rd | 124 +++++++-------- man/FEVData.Rd | 42 ++--- man/L.Rd | 122 +++++++------- man/MHData.Rd | 36 ++-- man/P.Rd | 87 +++++----- man/SUData.Rd | 40 ++-- man/add.poset.Rd | 113 ++++++------- man/as.data.frame.Rd | 88 +++++----- man/as.matrix.pim.summary.Rd | 59 +++---- man/classes.Rd | 190 +++++++++++------------ man/coef.Rd | 69 ++++---- man/confint.pim.Rd | 61 +++---- man/create.poset.Rd | 56 +++--- man/estimators.Rd | 241 +++++++++++++++-------------- man/formula.Rd | 107 ++++++------ man/getters-pim.formula.Rd | 159 +++++++++---------- man/has.intercept.Rd | 137 ++++++++-------- man/is.complete.Rd | 70 ++++---- man/make.posfun.Rd | 38 ++-- man/model.matrix.pim.Rd | 133 ++++++++-------- man/new.pim.Rd | 36 ++-- man/new.pim.env.Rd | 180 +++++++++++---------- man/new.pim.formula.Rd | 133 +++++++--------- man/new.pim.poset.Rd | 237 +++++++++++++--------------- man/nobs.Rd | 87 +++++----- man/penv.Rd | 101 ++++++------ man/pim-class.Rd | 94 +++++------ man/pim-getters.Rd | 83 ++++------ man/pim-package.Rd | 42 ++--- man/pim.Rd | 355 +++++++++++++++++++++---------------------- man/pim.environment-class.Rd | 90 +++++----- man/pim.fit.Rd | 131 ++++++++------- man/pim.formula-class.Rd | 150 +++++++++--------- man/pim.poset-class.Rd | 64 +++---- man/pim.summary-class.Rd | 90 +++++----- man/pimdata.Rd | 50 +++--- man/poset.Rd | 117 +++++++------- man/print.Rd | 99 +++++------ man/response.Rd | 90 +++++----- man/sandwich.estimator.Rd | 77 +++++---- man/summary.pim.Rd | 67 +++----- man/vcov.Rd | 68 ++++---- man/vcov.estimators.Rd | 112 ++++++------- man/vcov.internal.Rd | 67 +++----- 69 files changed, 2812 insertions(+), 2804 deletions(-)
Title: Combining Matching and Linear Regression for Causal Inference
Description: Core functions as well as diagnostic and calibration tools for combining matching and linear regression for causal inference in observational studies.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between MatchLinReg versions 0.7.0 dated 2015-07-12 and 0.7.3 dated 2020-02-03
ChangeLog |only DESCRIPTION | 8 +- MD5 | 7 +- man/mlr.match.Rd | 175 +++++++++++++++++++++++++++---------------------------- man/mlr.power.Rd | 114 +++++++++++++++++------------------ 5 files changed, 152 insertions(+), 152 deletions(-)
Title: Extra Additive Terms for Generalized Additive Models for
Location Scale and Shape
Description: Interface for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby, Vlasios Voudouris, Daniil Kiose
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.add versions 5.1-5 dated 2020-01-19 and 5.1-6 dated 2020-02-03
DESCRIPTION | 8 ++-- MD5 | 24 ++++++------- build/partial.rdb |binary man/centilesTwo.Rd | 6 ++- man/fitFixedKnots.Rd | 14 ++++--- man/fk.Rd | 2 - man/ga.Rd | 11 +++--- man/gamlss.add-package.Rd | 14 ++++--- man/gamlss.fk.Rd | 84 ++++++++++++++++++++++++---------------------- man/gamlss.ga.Rd | 11 +++--- man/gamlss.nn.Rd | 13 ++++--- man/nn.Rd | 24 ++++++------- man/tr.Rd | 16 ++++++-- 13 files changed, 128 insertions(+), 99 deletions(-)
Title: Diversity Estimator
Description: Contains functions for the 'DivE' estimator <doi:10.1371/journal.pcbi.1003646>. The 'DivE' estimator is a heuristic approach to estimate the number of classes or the number of species (species richness) in a population.
Author: Daniel J. Laydon, Aaron Sim, Charles R.M. Bangham, Becca Asquith
Maintainer: Daniel Laydon <d.laydon@imperial.ac.uk>
Diff between DivE versions 1.1 dated 2019-09-19 and 1.2 dated 2020-02-03
DESCRIPTION | 8 MD5 | 4 R/DivE.R | 1668 +++++++++++++++++++++++++++++++----------------------------- 3 files changed, 875 insertions(+), 805 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity from multidimensional matrices. Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several basic statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.3.3 dated 2019-12-06 and 1.3.5 dated 2020-02-03
DESCRIPTION | 13 ++++++------- MD5 | 15 ++++++++------- NAMESPACE | 7 ++++--- NEWS.md | 5 ++++- R/dispRity-package.R | 1 - R/morpho.utilities.R | 3 +-- R/zzz.R | 2 +- man/apply.NA.Rd | 2 -- src/char.diff.hamming.c |only 9 files changed, 24 insertions(+), 24 deletions(-)
Title: Subgroup Discovery and Bump Hunting
Description: Developed to assist in discovering interesting subgroups in high-dimensional data.
The PRIM implementation is based on the 1998 paper "Bump hunting in high-dimensional data" by Jerome H. Friedman and Nicholas I. Fisher <doi:10.1023/A:1008894516817>.
PRIM involves finding a set of "rules" which combined imply unusually large values of some other target variable.
Specifically one tries to find a set of sub regions in which the target variable is substantially larger than overall mean.
The objective of bump hunting in general is to find regions in the input (attribute/feature) space with relatively high values for the target variable.
The regions are described by simple rules of the type if: condition-1 and ... and condition-n then: estimated target value. Given the data (or a subset of the data),
the goal is to produce a box B within which the target mean is as large as possible.
Author: Jurian Baas [aut, cre, cph],
Ad Feelders [ctb]
Maintainer: Jurian Baas <j.baas@uu.nl>
Diff between subgroup.discovery versions 0.2.1 dated 2019-06-21 and 0.3.0 dated 2020-02-03
subgroup.discovery-0.2.1/subgroup.discovery/man/plot.prim.cover.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/plot.prim.diversify.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/plot.prim.validate.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/predict.prim.cover.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.box.optimal.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.candidates.find.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.cover.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.diversify.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.diversify.compare.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.peel.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.rule.condense.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.rule.match.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.rule.operations.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.validate.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/prim.validate.metrics.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/quasi.convex.hull.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/summary.prim.cover.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/summary.prim.diversify.Rd |only subgroup.discovery-0.2.1/subgroup.discovery/man/summary.prim.validate.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/DESCRIPTION | 28 subgroup.discovery-0.3.0/subgroup.discovery/MD5 | 59 subgroup.discovery-0.3.0/subgroup.discovery/NAMESPACE | 54 subgroup.discovery-0.3.0/subgroup.discovery/NEWS.md |only subgroup.discovery-0.3.0/subgroup.discovery/R/RcppExports.R |only subgroup.discovery-0.3.0/subgroup.discovery/R/data.R | 352 + subgroup.discovery-0.3.0/subgroup.discovery/R/prim.R | 1820 ++-------- subgroup.discovery-0.3.0/subgroup.discovery/R/subgroup.discovery.R |only subgroup.discovery-0.3.0/subgroup.discovery/README.md | 92 subgroup.discovery-0.3.0/subgroup.discovery/man/ames.Rd | 212 - subgroup.discovery-0.3.0/subgroup.discovery/man/credit.Rd | 50 subgroup.discovery-0.3.0/subgroup.discovery/man/pima.Rd | 122 subgroup.discovery-0.3.0/subgroup.discovery/man/plot.prim.peel.Rd | 44 subgroup.discovery-0.3.0/subgroup.discovery/man/plot.prim.predict.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/man/predict.prim.peel.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/man/prim.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/man/prim.box.index.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/man/prim.data.prepare.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/man/summary.prim.peel.Rd | 52 subgroup.discovery-0.3.0/subgroup.discovery/man/summary.prim.predict.Rd |only subgroup.discovery-0.3.0/subgroup.discovery/src |only subgroup.discovery-0.3.0/subgroup.discovery/tests/testthat.R | 8 subgroup.discovery-0.3.0/subgroup.discovery/tests/testthat/testPrim.R | 94 42 files changed, 1106 insertions(+), 1881 deletions(-)
More information about subgroup.discovery at CRAN
Permanent link
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.18 dated 2019-12-14 and 0.10.19 dated 2020-02-03
DESCRIPTION | 7 - MD5 | 60 +++++++------- NAMESPACE | 2 NEWS.md | 5 + R/data-type.R | 1 cleanup | 2 configure | 16 ++- man/MySQLConnection-class.Rd | 3 man/MySQLDriver-class.Rd | 7 - man/MySQLResult-class.Rd | 3 man/constants.Rd | 28 +++--- man/db-meta.Rd | 10 -- man/dbApply.Rd | 29 +++--- man/dbColumnInfo-MySQLConnection-method.Rd | 4 man/dbConnect-MySQLDriver-method.Rd | 24 +++-- man/dbDataType-MySQLDriver-method.Rd | 8 - man/dbEscapeStrings.Rd | 4 man/dbGetInfo-MySQLDriver-method.Rd | 8 - man/dbNextResult.Rd | 8 - man/dbQuoteIdentifier-MySQLConnection-character-method.Rd | 4 man/dbReadTable.Rd | 13 +-- man/dbUnloadDriver-MySQLDriver-method.Rd | 4 man/dbWriteTable.Rd | 42 +++++++-- man/isIdCurrent.Rd | 10 -- man/make.db.names-MySQLConnection-character-method.Rd | 25 +++-- man/mysqlBuildTableDefinition.Rd | 13 ++- man/mysqlClientLibraryVersions.Rd | 3 man/mysqlHasDefault.Rd | 3 man/query.Rd | 16 +-- man/result-meta.Rd | 14 +-- man/transactions.Rd | 8 - 31 files changed, 198 insertions(+), 186 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) <doi:10.18637/jss.v090.c01>.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.2.3 dated 2019-08-01 and 1.2.4 dated 2020-02-03
DESCRIPTION | 8 MD5 | 20 NEWS | 8 inst/doc/color-deficits.R | 30 - inst/doc/color-deficits.html | 725 ++++++++++++++------------------ inst/doc/creatingPalettes.R | 40 - inst/doc/creatingPalettes.html | 902 +++++++++++++++++++++-------------------- inst/doc/polychrome.R | 26 - inst/doc/polychrome.html | 591 ++++++++++++-------------- tests/testXform.R | 2 tests/testXform.Rout.save | 10 11 files changed, 1138 insertions(+), 1224 deletions(-)
Title: Add Multiple Colors to your Console & RMarkdown Output
Description: Add multiple colors to text that is printed to the console.
Author: Amanda Dobbyn [aut, cre],
Hernando Cortina [aut] (<https://orcid.org/0000-0001-6790-4870>)
Maintainer: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>
Diff between multicolor versions 0.1.3 dated 2019-04-13 and 0.1.4 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/rmd.R | 16 ++++++++-------- inst/doc/rmd.html | 22 +++++++++++++--------- man/crawl.Rd | 12 +++++++++--- man/multi_color.Rd | 12 +++++++++--- man/multi_colour.Rd | 12 +++++++++--- man/nix_first_newline.Rd | 2 +- man/things.Rd | 2 +- tests/testthat/test-multicolor.R | 34 ++++++++++++++++++---------------- 12 files changed, 87 insertions(+), 59 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas
Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>,
contains copies of lattice functions written by Deepayan Sarkar
<deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.28.0 dated 2019-11-11 and 1.28.1 dated 2020-02-03
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/hexagon_binning.pdf |binary man/gplot.hexbin.Rd | 5 +++-- 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Produce Descriptive and Comparative Tables Easily
Description: Easily create descriptive and comparative tables.
It makes use and integrates directly with the tidyverse family of packages, and pipes.
Tables are produced as data frames/lists of data frames for easy manipulation after creation,
and ready to be saved as csv, or piped to DT::datatable() or pander::pander() to integrate into reports.
Author: Maxime Wack [aut, cre],
Adrien Boukobza [aut]
Maintainer: Maxime Wack <maximewack@free.fr>
Diff between desctable versions 0.1.6 dated 2019-04-01 and 0.1.7 dated 2020-02-03
DESCRIPTION | 14 MD5 | 38 - NEWS | 4 R/build.R | 30 - R/convenience_functions.R | 4 R/output.R | 12 R/stats.R | 4 R/tests.R | 8 R/utils.R | 48 - README.md | 273 +++++----- build/vignette.rds |binary inst/doc/desctable.R | 84 +-- inst/doc/desctable.Rmd | 44 - inst/doc/desctable.html | 1148 ++++++++++++++++++++++++++-------------------- man/chisq.test.Rd | 24 man/datatable.Rd | 62 +- man/desctable.Rd | 12 man/fisher.test.Rd | 31 + man/pander.desctable.Rd | 13 vignettes/desctable.Rmd | 44 - 20 files changed, 1067 insertions(+), 830 deletions(-)
Title: A Monte Carlo Valuation Framework for Variable Annuities
Description: Implementation of a Monte Carlo simulation engine for valuing synthetic portfolios of
variable annuities, which reflect realistic features of common annuity contracts in practice.
It aims to facilitate the development and dissemination of research related to the efficient
valuation of a portfolio of large variable annuities. The main valuation methodology was
proposed by Gan (2017) <doi:10.1515/demo-2017-0021>.
Author: Hengxin Li [aut, cph],
Ben Feng [aut, cph],
Mingyi Jiang [aut, cph, cre],
GuoJun Gan [ctb]
Maintainer: Mingyi Jiang <m64jiang@uwaterloo.ca>
Diff between vamc versions 0.1.1 dated 2020-01-20 and 0.2.0 dated 2020-02-03
DESCRIPTION | 6 MD5 | 65 - NEWS.md |only R/Step1_YieldCurveGeneration.R | 1361 ++++++++++++++++++----------------- R/Step2_ScenarioGeneration.R | 9 R/Step3_PolicyGeneration.R | 8 R/Step4_MonteCarloValuation.R | 22 R/data.R | 398 +++++----- build/partial.rdb |binary inst/doc/my-vignette.R | 7 inst/doc/my-vignette.Rmd | 9 inst/doc/my-vignette.html | 42 - man/VAPort.Rd | 2 man/ageOnePolicy.Rd | 6 man/agePortfolio.Rd | 6 man/buildCurve.Rd | 65 + man/cForwardCurve.Rd | 2 man/calcMortFactors.Rd | 5 man/fundMap.Rd | 2 man/genFundScen.Rd | 3 man/genIndexScen.Rd | 6 man/genPortInception.Rd | 7 man/histDates.Rd | 2 man/histIdxScen.Rd | 2 man/indexNames.Rd | 2 man/indexScen.Rd | 2 man/mCov.Rd | 2 man/mortTable.Rd | 2 man/swapRate.Rd | 2 man/valuateOnePolicy.Rd | 4 man/valuatePortfolio.Rd | 5 tests/testthat/testBuildCurve.R | 11 tests/testthat/testCalcMortFactors.R | 64 - vignettes/my-vignette.Rmd | 9 34 files changed, 1128 insertions(+), 1010 deletions(-)
Title: 'jQuery UI' Interactions and Effects for Shiny
Description: An extension to shiny that brings interactions and animation effects from
'jQuery UI' library.
Author: Yang Tang [aut, cre]
Maintainer: Yang Tang <tang_yang@outlook.com>
Diff between shinyjqui versions 0.3.2 dated 2018-07-25 and 0.3.3 dated 2020-02-03
DESCRIPTION | 8 MD5 | 70 ++-- NAMESPACE | 2 NEWS.md | 9 R/icon.R |only R/includeJqueryUI.R | 2 R/interactions.R | 2 R/sortableCheckboxGroupInput.R | 4 R/sortableRadioButtons.R | 4 R/utils.R | 96 ++---- R/zzz.R |only build/vignette.rds |binary inst/doc/introduction.R | 34 +- inst/doc/introduction.html | 558 ++++++++++++++++++++++++++------------ inst/doc/orderInput.R | 12 inst/doc/orderInput.html | 399 +++++++++++++++++++++------ inst/doc/save-and-restore.R | 10 inst/doc/save-and-restore.Rmd | 6 inst/doc/save-and-restore.html | 434 ++++++++++++++++++++++------- inst/www/shinyjqui.js | 37 +- inst/www/shinyjqui.min.js | 2 man/Animation_effects.Rd | 138 ++++----- man/Class_effects.Rd | 146 +++++---- man/Interactions.Rd | 383 +++++++++++++------------- man/draggableModalDialog.Rd | 75 ++--- man/get_jqui_effects.Rd | 26 - man/includeJqueryUI.Rd | 58 +-- man/jqui_bookmarking.Rd | 28 - man/jqui_icon.Rd | 58 +-- man/orderInput.Rd | 144 +++++---- man/reexports.Rd | 30 +- man/selectableTableOutput.Rd | 96 +++--- man/sortableCheckboxGroupInput.Rd | 158 +++++----- man/sortableRadioButtons.Rd | 160 +++++----- man/sortableTableOutput.Rd | 76 ++--- man/sortableTabsetPanel.Rd | 123 ++++---- vignettes/save-and-restore.Rmd | 6 37 files changed, 2072 insertions(+), 1322 deletions(-)
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.0-81 dated 2020-01-17 and 1.0-82 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sdm.R | 1 + man/coordinates.Rd | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Pedigree-based Relatedness Coefficients
Description: Recursive algorithms for computing various relatedness coefficients,
including pairwise kinship, kappa and identity coefficients. Both autosomal
and X-linked coefficients are computed. Founders are allowed to be inbred.
In addition to the standard pairwise coefficients, ribd also computes a range
of lesser-known coefficients, including generalised kinship coefficients
(Karigl (1981) <doi:10.1111/j.1469-1809.1981.tb00341.x>; Weeks and
Lange (1988) <https:www.ncbi.nlm.nih.gov/pmc/articles/PMC1715269>),
two-locus coefficients (Thompson (1988) <doi:10.1093/imammb/5.4.261>) and
multi-person coefficients. This package is part of the ped suite,
a collection of packages for pedigree analysis with 'pedtools' as the core
package for creating and handling pedigree objects.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ribd versions 1.0.0 dated 2019-11-01 and 1.0.1 dated 2020-02-03
DESCRIPTION | 8 MD5 | 42 ++-- NAMESPACE | 2 NEWS.md | 4 R/kappaIBD.R | 121 ++++++------ man/condensedIdentity.Rd | 127 ++++++------- man/condensedIdentityX.Rd | 130 ++++++------- man/external_coefs.Rd | 188 +++++++++---------- man/generalisedKinship.Rd | 135 ++++++-------- man/generalised_karigl.Rd | 149 ++++++++------- man/inbreeding.Rd | 118 ++++++------ man/jicaque.Rd | 52 ++--- man/kappaIBD.Rd | 200 ++++++++++---------- man/kinPattern.Rd | 48 ++--- man/kinship.Rd | 90 ++++----- man/minimalPattern.Rd | 42 ++-- man/multiPersonIBD.Rd | 170 ++++++++--------- man/ribd.Rd | 23 +- man/twoLocusIBD.Rd | 441 +++++++++++++++++++++++----------------------- man/twoLocusIdentity.Rd | 145 +++++++-------- man/twoLocusKinship.Rd | 172 +++++++++-------- man/twoLocusPlot.Rd | 205 +++++++++++---------- 22 files changed, 1322 insertions(+), 1290 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.3.6 dated 2019-02-06 and 0.3.7 dated 2020-02-03
DESCRIPTION | 10 MD5 | 158 +++++------ NAMESPACE | 2 NEWS | 11 R/01supporting_functions.r | 14 - R/06PTModule.r | 2 R/07PTBlock.r | 4 R/10ModArchiveHelpers.r | 6 R/11MODPlugHelpers.r | 4 man/MODPlugToPTPattern.Rd | 268 ++++++++++--------- man/PTBlock.Rd | 147 +++++----- man/PTCell-class.Rd | 173 ++++++------ man/PTCell-method.Rd | 243 ++++++++--------- man/PTModule-class.Rd | 204 +++++++-------- man/PTPattern-class.Rd | 124 ++++----- man/PTPattern-method.Rd | 192 +++++++------- man/PTPatternToMODPlug.Rd | 148 +++++----- man/PTSample-class.Rd | 236 ++++++++--------- man/PTSample-method.Rd | 198 +++++++------- man/PTTrack-class.Rd | 126 ++++----- man/PTTrack-method.Rd | 205 +++++++-------- man/ProTrackR.Rd | 375 +++++++++++++-------------- man/appendPattern.Rd | 176 ++++++------ man/as.character.Rd | 149 +++++----- man/as.raw.Rd | 239 ++++++++--------- man/clearSamples.Rd | 103 ++++--- man/clearSong.Rd | 105 ++++--- man/deletePattern.Rd | 166 ++++++------ man/effect.Rd | 146 +++++----- man/fineTune.Rd | 132 +++++---- man/fix.PTModule.Rd | 163 ++++++----- man/funk_table.Rd | 44 +-- man/loopLength.Rd | 161 ++++++----- man/loopSample.Rd | 134 +++++---- man/loopStart.Rd | 159 ++++++----- man/loopState.Rd | 118 ++++---- man/mod.intro.Rd | 72 ++--- man/modArchive.Rd | 612 +++++++++++++++++++++++---------------------- man/modLand.Rd | 196 +++++++------- man/modToWave.Rd | 289 +++++++++++---------- man/moduleSize.Rd | 135 +++++---- man/name.Rd | 177 ++++++------- man/note.Rd | 192 +++++++------- man/noteManipulation.Rd | 221 ++++++++-------- man/noteToPeriod.Rd | 110 ++++---- man/nybble.Rd | 154 +++++------ man/nybbleToSignedInt.Rd | 140 +++++----- man/octave.Rd | 169 ++++++------ man/pasteBlock.Rd | 165 ++++++------ man/patternLength.Rd | 126 +++++---- man/patternOrder.Rd | 272 ++++++++++---------- man/patternOrderLength.Rd | 172 ++++++------ man/paula_clock.Rd | 58 ++-- man/periodToChar.Rd | 105 ++++--- man/period_table.Rd | 70 ++--- man/playMod.Rd | 134 +++++---- man/playSample.Rd | 213 ++++++++------- man/playWave.Rd | 114 ++++---- man/playingtable.Rd | 241 +++++++++-------- man/plot.Rd | 98 +++---- man/print.Rd | 98 +++---- man/proTrackerVibrato.Rd | 74 ++--- man/rawToCharNull.Rd | 112 ++++---- man/rawToPTModule.Rd | 151 +++++------ man/rawToSignedInt.Rd | 104 ++++--- man/rawToUnsignedInt.Rd | 112 ++++---- man/read.module.Rd | 199 +++++++------- man/read.sample.Rd | 155 ++++++----- man/resample.Rd | 88 +++--- man/sampleLength.Rd | 97 +++---- man/sampleNumber.Rd | 122 ++++---- man/sampleRate.Rd | 157 ++++++----- man/signedIntToNybble.Rd | 142 +++++----- man/signedIntToRaw.Rd | 108 ++++--- man/trackerFlag.Rd | 162 ++++++----- man/unsignedIntToRaw.Rd | 126 ++++----- man/volume.Rd | 130 +++++---- man/waveform.Rd | 239 +++++++++-------- man/write.module.Rd | 148 +++++----- man/write.sample.Rd | 143 +++++----- 80 files changed, 6119 insertions(+), 5628 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A lightweight, but comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data. Pedigrees
can be read from text files or created on the fly with built-in functions.
A range of utilities enable modifications like adding or removing individuals,
breaking loops, and merging pedigrees. Pedigree plots are produced by wrapping
the plotting functionality of the 'kinship2' package.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 0.9.1 dated 2019-12-02 and 0.9.2 dated 2020-02-03
DESCRIPTION | 8 MD5 | 112 ++++----- NAMESPACE | 4 NEWS.md | 10 R/marker_allelematrix.R | 4 R/marker_transfer.R | 4 R/mendelianCheck.R | 3 R/ped.R | 1 R/ped_accessors.R | 52 ++++ R/ped_plot.R | 12 - R/ped_utils.R | 2 build/vignette.rds |binary inst/doc/pedtools.html | 15 - man/as.data.frame.ped.Rd | 84 +++---- man/as.matrix.ped.Rd | 152 ++++++------- man/as.ped.Rd | 168 +++++++------- man/connectedComponents.Rd | 66 ++--- man/deprecated.Rd | 78 +++--- man/famid.Rd | 72 +++--- man/founderInbreeding.Rd | 100 ++++---- man/freqDatabase.Rd | 126 +++++----- man/getAlleles.Rd | 152 ++++++------- man/getComponent.Rd | 58 ++-- man/getMap.Rd | 57 ++-- man/getSex.Rd | 82 +++---- man/inbreedingLoops.Rd | 205 ++++++++--------- man/is.marker.Rd | 38 +-- man/is.ped.Rd | 96 ++++---- man/locusAttributes.Rd | 198 ++++++++--------- man/marker.Rd | 177 ++++++++------- man/marker_attach.Rd | 184 ++++++++------- man/marker_getset.Rd | 396 +++++++++++++++++----------------- man/marker_prop.Rd | 326 +++++++++++++-------------- man/marker_select.Rd | 108 ++++----- man/mendelianCheck.Rd | 80 +++--- man/mergePed.Rd | 100 ++++---- man/nMarkers.Rd | 48 ++-- man/ped.Rd | 208 +++++++++-------- man/ped_basic.Rd | 261 +++++++++++----------- man/ped_complex.Rd | 165 +++++++------- man/ped_internal.Rd | 132 +++++------ man/ped_modify.Rd | 229 ++++++++++--------- man/ped_subgroups.Rd | 229 +++++++++---------- man/ped_utils.Rd | 188 ++++++++-------- man/pedtools.Rd | 17 - man/plot.ped.Rd | 288 +++++++++++++----------- man/plotPedList.Rd | 256 +++++++++++---------- man/print.nucleus.Rd | 30 +- man/print.ped.Rd | 54 ++-- man/randomPed.Rd | 75 +++--- man/readPed.Rd | 207 +++++++++-------- man/relabel.Rd | 96 ++++---- man/sortGenotypes.Rd | 74 +++--- man/transferMarkers.Rd | 127 +++++----- man/validatePed.Rd | 36 +-- man/writePed.Rd | 97 ++++---- tests/testthat/test-mendelian-check.R | 1 57 files changed, 3165 insertions(+), 2983 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph],
Robert Rigby [aut],
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb],
Fernanda De Bastiani [ctb],
Raydonal Ospina [ctb],
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [ctb],
Marco Enea [ctb],
Alexios Ghalanos [ctb],
Christos Argyropoulos [ctb],
Almond Stocker [ctb],
Jens Lichter [ctb],
Stanislaus Stadlmann [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.1-5 dated 2019-10-04 and 5.1-6 dated 2020-02-03
DESCRIPTION | 8 MD5 | 12 R/Functions_for_SK_in_gamlss.R | 223 +++++++++++++--- R/SEP2.R | 553 ++++++++++++++++++++--------------------- build/partial.rdb |binary man/ST1.Rd | 4 man/momentSK.Rd | 9 7 files changed, 473 insertions(+), 336 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 5.1-5 dated 2019-10-06 and 5.1-6 dated 2020-02-03
DESCRIPTION | 8 +-- MD5 | 18 +++---- R/FitTail.R | 43 ++++++++++++++-- R/gamlss.R | 2 R/gamlssML.R | 7 +- R/gamlssVGD.R | 138 +++++++++++++++++++++++++++--------------------------- R/pb.R | 8 +-- build/partial.rdb |binary inst/doc/NEWS.txt | 33 ++++++++---- man/loglogSurv.Rd | 5 + 10 files changed, 152 insertions(+), 110 deletions(-)
Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre] (<https://orcid.org/0000-0002-1256-3375>),
David Firth [aut] (<https://orcid.org/0000-0003-0302-2312>),
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between gnm versions 1.1-0 dated 2018-06-21 and 1.1-1 dated 2020-02-03
gnm-1.1-0/gnm/data/House2001.R |only gnm-1.1-0/gnm/data/backPain.R |only gnm-1.1-0/gnm/data/barley.R |only gnm-1.1-0/gnm/data/barleyHeights.R |only gnm-1.1-0/gnm/data/cautres.R |only gnm-1.1-0/gnm/data/erikson.R |only gnm-1.1-0/gnm/data/friend.R |only gnm-1.1-0/gnm/data/mentalHealth.R |only gnm-1.1-0/gnm/data/voting.R |only gnm-1.1-0/gnm/data/wheat.R |only gnm-1.1-0/gnm/data/yaish.R |only gnm-1.1-0/gnm/tests/RC.R |only gnm-1.1-0/gnm/tests/RC.Rout.save |only gnm-1.1-0/gnm/tests/RChomog.R |only gnm-1.1-0/gnm/tests/RChomog.Rout.save |only gnm-1.1-0/gnm/tests/biplot.R |only gnm-1.1-0/gnm/tests/biplot.Rout.save |only gnm-1.1-0/gnm/tests/bwt.R |only gnm-1.1-0/gnm/tests/bwt.Rout.save |only gnm-1.1-0/gnm/tests/diagonalRef.R |only gnm-1.1-0/gnm/tests/diagonalRef.Rout.save |only gnm-1.1-0/gnm/tests/doubleUnidiff.R |only gnm-1.1-0/gnm/tests/doubleUnidiff.Rout.save |only gnm-1.1-0/gnm/tests/gammi.R |only gnm-1.1-0/gnm/tests/gammi.Rout.save |only gnm-1.1-0/gnm/tests/logexcess.R |only gnm-1.1-0/gnm/tests/logexcess.Rout.save |only gnm-1.1-0/gnm/tests/logistic.R |only gnm-1.1-0/gnm/tests/logistic.Rout.save |only gnm-1.1-0/gnm/tests/nls.R |only gnm-1.1-0/gnm/tests/nls.Rout.save |only gnm-1.1-0/gnm/tests/stereotype.R |only gnm-1.1-0/gnm/tests/stereotype.Rout.save |only gnm-1.1-0/gnm/tests/unidiff.R |only gnm-1.1-0/gnm/tests/unidiff.Rout.save |only gnm-1.1-1/gnm/DESCRIPTION | 8 gnm-1.1-1/gnm/MD5 | 103 - gnm-1.1-1/gnm/NAMESPACE | 170 +- gnm-1.1-1/gnm/NEWS.md | 1805 ++++++++++++++-------------- gnm-1.1-1/gnm/R/confint.profile.gnm.R | 4 gnm-1.1-1/gnm/R/getContrasts.R | 2 gnm-1.1-1/gnm/R/gnm.R | 694 +++++----- gnm-1.1-1/gnm/R/gnmTerms.R | 372 ++--- gnm-1.1-1/gnm/R/pickCoef.R | 2 gnm-1.1-1/gnm/R/predict.gnm.R | 338 ++--- gnm-1.1-1/gnm/R/residSVD.R | 4 gnm-1.1-1/gnm/R/update.gnm.R | 6 gnm-1.1-1/gnm/README.md | 29 gnm-1.1-1/gnm/TODO |only gnm-1.1-1/gnm/build/vignette.rds |binary gnm-1.1-1/gnm/data/House2001.rda |only gnm-1.1-1/gnm/data/backPain.rda |only gnm-1.1-1/gnm/data/barley.rda |only gnm-1.1-1/gnm/data/barleyHeights.rda |only gnm-1.1-1/gnm/data/cautres.rda |only gnm-1.1-1/gnm/data/erikson.rda |only gnm-1.1-1/gnm/data/friend.rda |only gnm-1.1-1/gnm/data/mentalHealth.rda |only gnm-1.1-1/gnm/data/voting.rda |only gnm-1.1-1/gnm/data/wheat.rda |only gnm-1.1-1/gnm/data/yaish.rda |only gnm-1.1-1/gnm/inst/WORDLIST | 440 +++--- gnm-1.1-1/gnm/inst/doc/gnmOverview.R | 1370 ++++++++++----------- gnm-1.1-1/gnm/inst/doc/gnmOverview.pdf |binary gnm-1.1-1/gnm/man/confint.gnm.Rd | 212 +-- gnm-1.1-1/gnm/man/gnm.Rd | 712 +++++------ gnm-1.1-1/gnm/man/pickCoef.Rd | 2 gnm-1.1-1/gnm/man/profile.gnm.Rd | 356 ++--- gnm-1.1-1/gnm/man/se.gnm.Rd | 142 +- gnm-1.1-1/gnm/tests/testthat |only 70 files changed, 3394 insertions(+), 3377 deletions(-)
Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called Databionic swarm (DBS) is introduced which was published in Thrun, M.C., Ultsch A.: "Swarm Intelligence for Self-Organized Clustering" (2020), Artificial Intelligence, <DOI:10.1016/j.artint.2020.103237>. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The comparison to common projection methods can be found in the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>. A comparison to 26 common clustering algorithms on 15 datasets is presented on the website.
Author: Michael Thrun [aut, cre, cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DatabionicSwarm versions 1.1.2 dated 2019-12-11 and 1.1.3 dated 2020-02-03
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- build/partial.rdb |binary inst/NEWS | 5 ++++- inst/doc/DatabionicSwarm.html | 21 ++++++++++++++------- man/DBSclustering.Rd | 5 ++--- man/DatabionicSwarm-package.Rd | 6 ++++-- man/Pswarm.Rd | 4 +++- 8 files changed, 40 insertions(+), 27 deletions(-)
More information about DatabionicSwarm at CRAN
Permanent link
Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner [aut, cre],
David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between BradleyTerry2 versions 1.1-0 dated 2019-05-11 and 1.1-2 dated 2020-02-03
BradleyTerry2-1.1-0/BradleyTerry2/data/CEMS.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/chameleons.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/citations.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/icehockey.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/seeds.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/sound.fields.R |only BradleyTerry2-1.1-0/BradleyTerry2/data/springall.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/BTabilities.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/BTabilities.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/add1.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/add1.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/baseball.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/baseball.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/countsToBinomial.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/countsToBinomial.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/flatlizards.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/flatlizards.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/nested.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/nested.Rout.save |only BradleyTerry2-1.1-0/BradleyTerry2/tests/predict.R |only BradleyTerry2-1.1-0/BradleyTerry2/tests/predict.Rout.save |only BradleyTerry2-1.1-2/BradleyTerry2/DESCRIPTION | 10 - BradleyTerry2-1.1-2/BradleyTerry2/MD5 | 94 +++++----- BradleyTerry2-1.1-2/BradleyTerry2/NEWS.md | 6 BradleyTerry2-1.1-2/BradleyTerry2/R/BTm.R | 9 BradleyTerry2-1.1-2/BradleyTerry2/R/BTm.setup.R | 31 +-- BradleyTerry2-1.1-2/BradleyTerry2/R/flatlizards.R | 26 +- BradleyTerry2-1.1-2/BradleyTerry2/R/predict.BTm.R | 10 - BradleyTerry2-1.1-2/BradleyTerry2/R/sound.fields.R | 4 BradleyTerry2-1.1-2/BradleyTerry2/README.md | 4 BradleyTerry2-1.1-2/BradleyTerry2/build/vignette.rds |binary BradleyTerry2-1.1-2/BradleyTerry2/data/CEMS.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/chameleons.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/citations.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/icehockey.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/seeds.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/sound.fields.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/springall.rda |only BradleyTerry2-1.1-2/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary BradleyTerry2-1.1-2/BradleyTerry2/man/BTm.Rd | 28 ++ BradleyTerry2-1.1-2/BradleyTerry2/man/GenDavidson.Rd | 16 + BradleyTerry2-1.1-2/BradleyTerry2/man/add1.BTm.Rd | 3 BradleyTerry2-1.1-2/BradleyTerry2/man/baseball.Rd | 4 BradleyTerry2-1.1-2/BradleyTerry2/man/citations.Rd | 2 BradleyTerry2-1.1-2/BradleyTerry2/man/flatlizards.Rd | 26 +- BradleyTerry2-1.1-2/BradleyTerry2/man/glmmPQL.Rd | 25 ++ BradleyTerry2-1.1-2/BradleyTerry2/man/glmmPQL.control.Rd | 3 BradleyTerry2-1.1-2/BradleyTerry2/man/icehockey.Rd | 4 BradleyTerry2-1.1-2/BradleyTerry2/man/plotProportions.Rd | 28 ++ BradleyTerry2-1.1-2/BradleyTerry2/man/predict.BTglmmPQL.Rd | 14 + BradleyTerry2-1.1-2/BradleyTerry2/man/predict.BTm.Rd | 15 + BradleyTerry2-1.1-2/BradleyTerry2/man/residuals.BTm.Rd | 8 BradleyTerry2-1.1-2/BradleyTerry2/man/sound.fields.Rd | 4 BradleyTerry2-1.1-2/BradleyTerry2/tests/old-tests |only BradleyTerry2-1.1-2/BradleyTerry2/tests/testthat |only BradleyTerry2-1.1-2/BradleyTerry2/tests/testthat.R |only 56 files changed, 235 insertions(+), 139 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-23 1.2
2015-07-17 1.1
2014-10-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-09 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-30 1.0-2
2017-06-28 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-14 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-21 0.99.1
2019-07-02 0.99.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-31 1.1.1
2019-06-02 1.1.0
2018-11-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-20 0.3
2018-11-08 0.2
2017-11-14 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-24 0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-24 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-28 1.3.0
2017-05-10 1.2.4
2016-07-22 1.2.3
2016-06-28 1.2.2
2016-06-22 1.2.1
2016-03-21 1.2
2015-11-12 1.1-1
2015-09-14 1.0-5
2015-07-16 1.0-4
2015-07-08 1.0-3
2015-05-22 1.0-1
2015-05-05 0.9-12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-18 0.9-11
2015-04-27 0.9-8
2013-12-13 0.9-4
2011-11-14 0.9-2
2011-11-11 0.9-0
2011-04-11 0.8-33
2010-11-29 0.8-32
2010-10-11 0.8-31
2010-09-19 0.8-30
2010-06-30 0.8-28
2010-05-16 0.8-27
2009-10-15 0.8-26
2009-04-15 0.8-25
2008-04-29 0.8-24
2008-04-24 0.8-23
2007-12-17 0.8-22
2007-11-20 0.8-21
2007-05-22 0.8-20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-27 1.7
2015-04-27 1.6.9
2013-08-22 1.6.7
2013-03-21 1.6.5
2013-03-16 1.6.4
2012-09-03 1.6.3
2012-01-03 1.6.2
2011-02-08 1.4
2011-02-08 1.5
2010-01-06 1.3
2009-11-06 1.2
2009-01-26 1.1
2007-11-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-09 0.2.0
2018-08-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-05 1.5.2
2019-05-07 1.5.1
2019-04-24 1.5
2018-07-11 1.4.2
2017-06-06 1.4.1
2016-10-16 1.4
2015-12-05 1.3.2
2015-11-25 1.3.1
2015-11-20 1.3
2015-09-17 1.2.3
2015-08-31 1.2.2
2015-08-13 1.2.1
2015-08-05 1.2
2015-06-09 1.1.5
2015-01-14 1.1.4
2014-12-11 1.1.3
2014-12-09 1.1.2
2014-12-02 1.1.1
2014-11-25 1.1
2014-10-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-08 2.1
2017-03-02 1.3
2016-12-04 1.2
2016-10-17 1.1
2016-10-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-06 0.2.8
2017-07-11 0.2.6
2017-04-08 0.2.4
2016-12-31 0.2.3
2016-10-12 0.2.2
2016-10-07 0.2.1
2016-09-06 0.2
2016-08-17 0.1
Title: Estimation of the Effective Dimension Reduction ('EDR') Space
Description: The library contains R-functions to estimate the effective
dimension reduction space in 'multi-index' regression models.
Author: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between EDR versions 0.6-6 dated 2016-09-14 and 0.6-7 dated 2020-02-03
DESCRIPTION | 10 ++--- MD5 | 9 ++-- NAMESPACE | 4 +- R/edr.r | 109 ++++++++++++++++++++++++++++++------------------------------ R/edrcv.r | 38 ++++++++++---------- src/init.c |only 6 files changed, 86 insertions(+), 84 deletions(-)
Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is the generalization of on an idea from the book "Projection-Based Clustering through Self-Organization and Swarm Intelligence" <DOI:10.1007/978-3-658-20540-9>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre, cph],
Florian Lerch [aut],
Felix Pape [aut],
Tim Schreier [aut],
Luis Winckelmann [aut],
Kristian Nybo [cph],
Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ProjectionBasedClustering versions 1.0.7 dated 2018-05-06 and 1.1.0 dated 2020-02-03
DESCRIPTION | 20 +++-- MD5 | 20 ++--- NAMESPACE | 8 +- R/PlotProjectedPoints.R | 1 R/RcppExports.R | 16 ++-- R/interactiveProjectionBasedClustering.R |only R/tSNE.R | 57 ++++++++++----- man/Hepta.Rd | 6 + man/ProjectionBasedClustering-package.Rd | 15 +--- man/interactiveProjectionBasedClustering.Rd |only man/tSNE.Rd | 105 ++++++++++++++++------------ src/RcppExports.cpp | 68 +++++++++--------- 12 files changed, 183 insertions(+), 133 deletions(-)
More information about ProjectionBasedClustering at CRAN
Permanent link
Title: Tools for Developing Binary Logistic Regression Models
Description: Tools designed to make it easier for beginner and intermediate users to build and validate
binary logistic regression models. Includes bivariate analysis, comprehensive regression output,
model fit statistics, variable selection procedures, model validation techniques and a 'shiny'
app for interactive model building.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between blorr versions 0.2.1 dated 2019-03-12 and 0.2.2 dated 2020-02-03
blorr-0.2.1/blorr/inst/application |only blorr-0.2.2/blorr/DESCRIPTION | 14 blorr-0.2.2/blorr/MD5 | 166 - blorr-0.2.2/blorr/NAMESPACE | 3 blorr-0.2.2/blorr/NEWS.md | 6 blorr-0.2.2/blorr/R/RcppExports.R | 14 blorr-0.2.2/blorr/R/blr-backward-elimination.R | 2 blorr-0.2.2/blorr/R/blr-launch-app.R | 6 blorr-0.2.2/blorr/R/blr-lorenz-curve.R | 2 blorr-0.2.2/blorr/R/blr-lrtest.R | 4 blorr-0.2.2/blorr/R/blr-output.R | 6 blorr-0.2.2/blorr/R/blr-stepwise-backward-regression.R | 4 blorr-0.2.2/blorr/R/blr-stepwise-regression.R | 10 blorr-0.2.2/blorr/R/blr-utils.R | 17 blorr-0.2.2/blorr/README.md | 11 blorr-0.2.2/blorr/build/vignette.rds |binary blorr-0.2.2/blorr/inst/doc/introduction.html | 891 +++++----- blorr-0.2.2/blorr/tests/figs/deps.txt | 9 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/c-fitted-plot.svg | 450 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/c-leverage-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/c-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/cbar-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/decile-capture-rate-chart.svg | 90 - blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/decile-lift-chart.svg | 86 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/deviance-fitted-plot.svg | 456 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/deviance-residual-plot.svg | 458 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difchisq-fitted-plot.svg | 458 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difchisq-leverage-plot.svg | 462 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difchisq-plot.svg | 462 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difdev-fitted-plot.svg | 450 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difdev-leverage-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/difdev-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/fitted-leverage-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/forward-selection-plot.svg | 53 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/ks-chart.svg | 190 +- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/leverage-fitted-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/leverage-plot.svg | 458 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/lift-chart.svg | 96 - blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/lorenz-curve.svg | 98 - blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/pearson-residual-plot.svg | 454 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/residual-fitted-plot.svg | 452 ++--- blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/roc-curve.svg | 118 - blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/segment-distribution-plot.svg | 84 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/stepwise-backward-selection-plot.svg | 55 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/stepwise-selection-plot.svg | 51 blorr-0.2.2/blorr/tests/figs/test-blr-plots-r/woe-plot.svg | 58 blorr-0.2.2/blorr/tests/testthat/test-bivariate-analysis.R | 83 blorr-0.2.2/blorr/tools/README-kschart-1.png |binary blorr-0.2.2/blorr/tools/README-lift-1.png |binary blorr-0.2.2/blorr/tools/README-roc-1.png |binary blorr-0.2.2/blorr/tools/README-unnamed-chunk-2-1.png |binary 51 files changed, 4864 insertions(+), 5101 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R.
Author: Ben Bolker [aut, cre],
R Development Core Team [aut],
Iago Giné-Vázquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.22 dated 2019-12-19 and 1.0.23.1 dated 2020-02-03
bbmle-1.0.22/bbmle/R/TMB.R |only bbmle-1.0.23.1/bbmle/DESCRIPTION | 8 +++---- bbmle-1.0.23.1/bbmle/MD5 | 13 +++++------- bbmle-1.0.23.1/bbmle/inst/NEWS.Rd | 8 ++++++- bbmle-1.0.23.1/bbmle/inst/doc/mle2.pdf |binary bbmle-1.0.23.1/bbmle/inst/doc/quasi.pdf |binary bbmle-1.0.23.1/bbmle/tests/profbound.R | 18 +++++++++++++---- bbmle-1.0.23.1/bbmle/tests/profbound.Rout.save | 26 +++++++++++++++++-------- 8 files changed, 49 insertions(+), 24 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapproj versions 1.2.6 dated 2018-03-29 and 1.2.7 dated 2020-02-03
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/mapproject.Rd | 2 +- src/cuts.c | 3 +++ src/guyou.c | 4 ++-- src/hex.c | 3 ++- src/map.h | 10 +++++----- src/tetra.c | 4 ++-- 8 files changed, 26 insertions(+), 22 deletions(-)
Title: Likelihood-Based Boosting for Generalized Mixed Models
Description: Likelihood-based boosting approaches for generalized mixed models are provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between GMMBoost versions 1.1.2 dated 2013-11-22 and 1.1.3 dated 2020-02-03
DESCRIPTION | 12 +++--- MD5 | 18 ++++----- NAMESPACE | 1 R/OrdinalBoost.r | 18 ++++----- R/bGAMM.r | 4 +- R/bGLMM.r | 102 ++++++++++++++++++++++++++-------------------------- R/bGLMMControl.r | 3 + man/GMMBoost.Rd | 16 ++++---- man/OrdinalBoost.rd | 4 +- man/knee.Rd | 68 +++++++++++++++++----------------- 10 files changed, 126 insertions(+), 120 deletions(-)
Title: Tools for Working with Connectivity Data
Description: Collects several different methods for analyzing and
working with connectivity data in R. Though primarily oriented towards
marine larval dispersal, many of the methods are general and useful for
terrestrial systems as well.
Author: David M. Kaplan <dmkaplan2000@gmail.com> [cre,aut], Marco Andrello <marco.andrello@gmail.com> [ctb]
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>
Diff between ConnMatTools versions 0.3.3 dated 2016-11-02 and 0.3.5 dated 2020-02-03
DESCRIPTION | 10 +-- MD5 | 86 +++++++++++++-------------- NEWS | 10 +++ R/ConnMatTools.R | 4 - R/Jacobi_EPT_reserve_selection.R | 2 R/connectivity_estimation.distributions.R | 2 R/dpr_model.R | 8 +- R/eigs.R | 2 R/jacobi_etal_2012.R | 2 man/BevertonHolt.Rd | 7 -- man/ConnMatTools.Rd | 16 ++--- man/DPRHomerangeGravity.Rd | 23 +++++-- man/DispersalPerRecruitModel.Rd | 17 +++-- man/betasVectorDefault.Rd | 7 -- man/chile.loco.Rd | 7 -- man/d.mix.dists.func.Rd | 7 -- man/d.rel.conn.beta.prior.Rd | 93 ++++++++++++++++++++---------- man/d.rel.conn.dists.func.Rd | 75 +++++++++++++++--------- man/d.rel.conn.finite.settlement.Rd | 48 ++++++++++----- man/d.rel.conn.multinomial.unnorm.Rd | 35 ++++++----- man/d.rel.conn.multiple.Rd | 85 ++++++++++++++++++--------- man/d.rel.conn.unif.prior.Rd | 30 +++++---- man/damselfish.lods.Rd | 7 -- man/dual.mark.transmission.Rd | 25 ++++---- man/eigs.Rd | 17 +++-- man/gammaParamsConvert.Rd | 1 man/hockeyStick.Rd | 7 -- man/laplacianConnMat.Rd | 7 -- man/localRetention.Rd | 1 man/mergeSubpops.Rd | 7 -- man/optim.rel.conn.dists.Rd | 38 +++++++----- man/optimalSplitConnMat.Rd | 20 ++++-- man/prob.marked.Rd | 7 -- man/protectedAreaSelection.Rd | 21 ++++-- man/qualitySubpops.Rd | 7 -- man/r.marked.egg.fraction.Rd | 47 +++++++++------ man/recSplitConnMat.Rd | 7 -- man/reducedConnMat.Rd | 7 -- man/relativeLocalRetention.Rd | 1 man/selfRecruitment.Rd | 1 man/settlerRecruitSlopeCorrection.Rd | 16 +++-- man/splitConnMat.Rd | 18 +++-- man/stepfun.hist.Rd | 13 +--- man/subpopsVectorToList.Rd | 7 -- 44 files changed, 510 insertions(+), 348 deletions(-)
Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including the single transferable vote (ranked choice), approval, score and plurality methods.
Author: Hana Sevcikova, Bernard Silverman, Adrian Raftery
Maintainer: Hana Sevcikova<hanas@uw.edu>
Diff between vote versions 1.2-0 dated 2020-01-30 and 1.2-1 dated 2020-02-03
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/stv.R | 40 +++++++++++++++++++++++++++++----------- data/ims_approval.rda |binary data/ims_plurality.rda |binary data/ims_score.rda |binary data/ims_stv.rda |binary man/stv.Rd | 3 ++- 9 files changed, 53 insertions(+), 24 deletions(-)
Title: Factor Analysis Controlling the Effects of Response Bias
Description: Vampirize the response biases from a dataset! Performs
factor analysis controlling the effects of social desirability
and acquiescence using the method described in Ferrando,
Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.
Author: David Navarro-Gonzalez, Andreu Vigil-Colet, Pere J. Ferrando, Urbano Lorenzo-Seva, Jorge N. Tendeiro
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>
Diff between vampyr versions 1.0.5 dated 2020-01-20 and 1.0.6 dated 2020-02-03
DESCRIPTION | 10 - MD5 | 10 - NAMESPACE | 1 R/ControlResponseBias.R | 429 ++++++++++++++++++++++++++++++++++++++++++++- man/ControlResponseBias.Rd | 14 + man/vampyr_example.Rd | 6 6 files changed, 445 insertions(+), 25 deletions(-)
Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.6.3 dated 2019-11-11 and 0.6.4 dated 2020-02-03
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 1 + NEWS.md | 6 +++++- R/checkInputs.R | 33 ++++++++++----------------------- R/shadow-package.R | 1 + R/shadowFootprint.R | 2 +- build/vignette.rds |binary man/SVF.Rd | 21 ++++++++++++++++----- man/inShadow.Rd | 34 +++++++++++++++++++++++++--------- man/plotGrid.Rd | 3 +-- man/radiation.Rd | 16 ++++++++++++---- man/shadow.Rd | 1 - man/shadowFootprint.Rd | 13 ++++++++----- man/shadowHeight.Rd | 29 ++++++++++++++++++++--------- man/surfaceGrid.Rd | 9 +++++++++ 17 files changed, 130 insertions(+), 81 deletions(-)
Title: Performs Common Linear Algebra Operations Used in Quantum
Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>. Can be used with the gridsynth algorithm <arXiv:1212.6253> to perform decomposition into the Clifford+T set.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Diff between QuantumOps versions 3.0.0 dated 2019-12-14 and 3.0.1 dated 2020-02-03
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + NEWS.md | 10 +++++++++- R/PhaseDamping.R |only R/QFT.R | 4 ++-- R/QuantumClassifier.R | 13 ++++++++++--- R/Shor.R | 11 ++++++++--- man/CoherentNoise.Rd | 2 +- man/FullAdder.Rd | 2 +- man/G.Rd | 2 +- man/PhaseDamping.Rd |only man/QFT.Rd | 3 ++- man/controlled.Rd | 4 ++-- man/convert_bin2dec.Rd | 2 +- man/measure.Rd | 2 +- 16 files changed, 59 insertions(+), 35 deletions(-)
Title: Create Pivot Tables
Description: Create regular pivot tables with just a few lines of R.
More complex pivot tables can also be created, e.g. pivot tables
with irregular layouts, multiple calculations and/or derived
calculations based on multiple data frames. Pivot tables are
constructed using R only and can be written to a range of
output formats (plain text, 'HTML', 'Latex' and 'Excel'),
including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>
Diff between pivottabler versions 1.2.3 dated 2019-11-01 and 1.3.0 dated 2020-02-03
pivottabler-1.2.3/pivottabler/inst/doc/v01-introduction.R |only pivottabler-1.2.3/pivottabler/inst/doc/v01-introduction.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v01-introduction.html |only pivottabler-1.2.3/pivottabler/inst/doc/v02-datagroups.R |only pivottabler-1.2.3/pivottabler/inst/doc/v02-datagroups.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v02-datagroups.html |only pivottabler-1.2.3/pivottabler/inst/doc/v03-calculations.R |only pivottabler-1.2.3/pivottabler/inst/doc/v03-calculations.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v03-calculations.html |only pivottabler-1.2.3/pivottabler/inst/doc/v04-outputs.R |only pivottabler-1.2.3/pivottabler/inst/doc/v04-outputs.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v04-outputs.html |only pivottabler-1.2.3/pivottabler/inst/doc/v05-latexoutput.R |only pivottabler-1.2.3/pivottabler/inst/doc/v05-latexoutput.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v05-latexoutput.html |only pivottabler-1.2.3/pivottabler/inst/doc/v06-styling.R |only pivottabler-1.2.3/pivottabler/inst/doc/v06-styling.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v06-styling.html |only pivottabler-1.2.3/pivottabler/inst/doc/v07-findingandformatting.R |only pivottabler-1.2.3/pivottabler/inst/doc/v07-findingandformatting.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v07-findingandformatting.html |only pivottabler-1.2.3/pivottabler/inst/doc/v08-cellcontext.R |only pivottabler-1.2.3/pivottabler/inst/doc/v08-cellcontext.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v08-cellcontext.html |only pivottabler-1.2.3/pivottabler/inst/doc/v09-irregularlayout.R |only pivottabler-1.2.3/pivottabler/inst/doc/v09-irregularlayout.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v09-irregularlayout.html |only pivottabler-1.2.3/pivottabler/inst/doc/v10-performance.R |only pivottabler-1.2.3/pivottabler/inst/doc/v10-performance.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v10-performance.html |only pivottabler-1.2.3/pivottabler/inst/doc/v11-shiny.R |only pivottabler-1.2.3/pivottabler/inst/doc/v11-shiny.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v11-shiny.html |only pivottabler-1.2.3/pivottabler/inst/doc/v12-excelexport.R |only pivottabler-1.2.3/pivottabler/inst/doc/v12-excelexport.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/v12-excelexport.html |only pivottabler-1.2.3/pivottabler/inst/doc/vA1-appendix.R |only pivottabler-1.2.3/pivottabler/inst/doc/vA1-appendix.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/vA1-appendix.html |only pivottabler-1.2.3/pivottabler/inst/doc/vA2-appendix.R |only pivottabler-1.2.3/pivottabler/inst/doc/vA2-appendix.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/vA2-appendix.html |only pivottabler-1.2.3/pivottabler/inst/doc/vA3-appendix.R |only pivottabler-1.2.3/pivottabler/inst/doc/vA3-appendix.Rmd |only pivottabler-1.2.3/pivottabler/inst/doc/vA3-appendix.html |only pivottabler-1.2.3/pivottabler/tests/testthat/test01_basicTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test02_smokeTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test03_illegalNameTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test04_quickPivotTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test05_basicLayoutTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test06_dataGroupTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test07_calculationTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test08_visualTotalTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test09_dataTypeTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test10_themingTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test11_emptyGroupTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test12_exportTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test13_latexTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test14_exportOptionsTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test15_findGrouptests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test16_getCellsTests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test17_findCellstests.R |only pivottabler-1.2.3/pivottabler/tests/testthat/test18_irregularLayoutTests.R |only pivottabler-1.2.3/pivottabler/vignettes/v01-introduction.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v02-datagroups.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v03-calculations.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v04-outputs.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v05-latexoutput.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v06-styling.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v07-findingandformatting.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v08-cellcontext.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v09-irregularlayout.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v10-performance.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v11-shiny.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/v12-excelexport.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/vA1-appendix.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/vA2-appendix.Rmd |only pivottabler-1.2.3/pivottabler/vignettes/vA3-appendix.Rmd |only pivottabler-1.3.0/pivottabler/DESCRIPTION | 13 pivottabler-1.3.0/pivottabler/MD5 | 269 +- pivottabler-1.3.0/pivottabler/NAMESPACE | 1 pivottabler-1.3.0/pivottabler/NEWS.md | 52 pivottabler-1.3.0/pivottabler/R/PivotBatchCalculator.R | 3 pivottabler-1.3.0/pivottabler/R/PivotCalculation.R | 12 pivottabler-1.3.0/pivottabler/R/PivotCalculationGroup.R | 8 pivottabler-1.3.0/pivottabler/R/PivotCalculator.R | 119 - pivottabler-1.3.0/pivottabler/R/PivotCell.R | 24 pivottabler-1.3.0/pivottabler/R/PivotCells.R | 33 pivottabler-1.3.0/pivottabler/R/PivotDataGroup.R | 962 +++++++--- pivottabler-1.3.0/pivottabler/R/PivotHtmlRenderer.R | 373 ++- pivottabler-1.3.0/pivottabler/R/PivotLatexRenderer.R | 14 pivottabler-1.3.0/pivottabler/R/PivotOpenXlsxRenderer.R | 160 + pivottabler-1.3.0/pivottabler/R/PivotStyles.R | 48 pivottabler-1.3.0/pivottabler/R/PivotTable.R | 698 ++++++- pivottabler-1.3.0/pivottabler/R/PivotThemes.R | 419 ++-- pivottabler-1.3.0/pivottabler/R/convertor.R | 132 + pivottabler-1.3.0/pivottabler/README.md | 30 pivottabler-1.3.0/pivottabler/build/vignette.rds |binary pivottabler-1.3.0/pivottabler/inst/doc/v00-vignettes.Rmd |only pivottabler-1.3.0/pivottabler/inst/doc/v00-vignettes.html |only pivottabler-1.3.0/pivottabler/man/PivotBatch.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotBatchCalculator.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotBatchStatistics.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotCalculation.Rd | 7 pivottabler-1.3.0/pivottabler/man/PivotCalculationGroup.Rd | 7 pivottabler-1.3.0/pivottabler/man/PivotCalculationGroups.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotCalculator.Rd | 21 pivottabler-1.3.0/pivottabler/man/PivotCell.Rd | 9 pivottabler-1.3.0/pivottabler/man/PivotCells.Rd | 13 pivottabler-1.3.0/pivottabler/man/PivotData.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotDataGroup.Rd | 69 pivottabler-1.3.0/pivottabler/man/PivotFilter.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotFilterOverrides.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotFilters.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotHtmlRenderer.Rd | 7 pivottabler-1.3.0/pivottabler/man/PivotLatexRenderer.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotOpenXlsxRenderer.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotOpenXlsxStyle.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotOpenXlsxStyles.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotStyle.Rd | 4 pivottabler-1.3.0/pivottabler/man/PivotStyles.Rd | 13 pivottabler-1.3.0/pivottabler/man/PivotTable.Rd | 97 - pivottabler-1.3.0/pivottabler/man/bhmtraindisruption.Rd | 74 pivottabler-1.3.0/pivottabler/man/bhmtrains.Rd | 84 pivottabler-1.3.0/pivottabler/man/checkArgument.Rd | 24 pivottabler-1.3.0/pivottabler/man/cleanCssValue.Rd | 40 pivottabler-1.3.0/pivottabler/man/containsText.Rd | 42 pivottabler-1.3.0/pivottabler/man/convertPvtStyleToBasicStyle.Rd | 40 pivottabler-1.3.0/pivottabler/man/convertPvtTblToBasicTbl.Rd | 11 pivottabler-1.3.0/pivottabler/man/exportValueAs.Rd | 8 pivottabler-1.3.0/pivottabler/man/getBlankTheme.Rd | 36 pivottabler-1.3.0/pivottabler/man/getCompactTheme.Rd | 36 pivottabler-1.3.0/pivottabler/man/getDefaultTheme.Rd | 36 pivottabler-1.3.0/pivottabler/man/getLargePlainTheme.Rd | 36 pivottabler-1.3.0/pivottabler/man/getNextPosition.Rd | 40 pivottabler-1.3.0/pivottabler/man/getPvtStyleDeclarations.Rd | 34 pivottabler-1.3.0/pivottabler/man/getSimpleColoredTheme.Rd | 8 pivottabler-1.3.0/pivottabler/man/getStandardTableTheme.Rd |only pivottabler-1.3.0/pivottabler/man/getTheme.Rd | 36 pivottabler-1.3.0/pivottabler/man/getXlBorderFromCssBorder.Rd | 40 pivottabler-1.3.0/pivottabler/man/getXlBorderStyleFromCssBorder.Rd | 38 pivottabler-1.3.0/pivottabler/man/isNumericValue.Rd | 34 pivottabler-1.3.0/pivottabler/man/isTextValue.Rd | 34 pivottabler-1.3.0/pivottabler/man/oneToNULL.Rd | 40 pivottabler-1.3.0/pivottabler/man/parseColor.Rd | 38 pivottabler-1.3.0/pivottabler/man/parseCssBorder.Rd | 38 pivottabler-1.3.0/pivottabler/man/parseCssSizeToPt.Rd | 42 pivottabler-1.3.0/pivottabler/man/parseCssSizeToPx.Rd | 42 pivottabler-1.3.0/pivottabler/man/parseCssString.Rd | 46 pivottabler-1.3.0/pivottabler/man/parseXlBorder.Rd | 38 pivottabler-1.3.0/pivottabler/man/pivottabler.Rd | 16 pivottabler-1.3.0/pivottabler/man/pivottablerOutput.Rd | 36 pivottabler-1.3.0/pivottabler/man/processIdentifier.Rd | 36 pivottabler-1.3.0/pivottabler/man/processIdentifiers.Rd | 36 pivottabler-1.3.0/pivottabler/man/pvtperfresults.Rd | 56 pivottabler-1.3.0/pivottabler/man/pvtperfsummary.Rd | 70 pivottabler-1.3.0/pivottabler/man/qhpvt.Rd | 16 pivottabler-1.3.0/pivottabler/man/qlpvt.Rd | 3 pivottabler-1.3.0/pivottabler/man/qpvt.Rd | 16 pivottabler-1.3.0/pivottabler/man/renderBasicTable.Rd | 3 pivottabler-1.3.0/pivottabler/man/renderPivottabler.Rd | 36 pivottabler-1.3.0/pivottabler/man/skipExportingValue.Rd | 42 pivottabler-1.3.0/pivottabler/man/trainstations.Rd | 56 pivottabler-1.3.0/pivottabler/tests/testthat/test-01-basicTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-02-smokeTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-03-illegalNameTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-04-quickPivotTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-05-basicLayoutTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-06-dataGroupTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-07-calculationTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-08-visualTotalTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-09-dataTypeTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-10-themingTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-11-emptyGroupTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-12-exportTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-13-latexTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-14-exportOptionsTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-15-findGrouptests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-16-getCellsTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-17-findCellstests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-18-irregularLayoutTests.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-19-calculationFormatting.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-20-dataGroupFormatting.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-21-alternativeLayouts.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-22-basicRowGroupHeaderLayouts.R |only pivottabler-1.3.0/pivottabler/tests/testthat/test-23-outlineLayouts.R |only pivottabler-1.3.0/pivottabler/vignettes/layout1.png |only pivottabler-1.3.0/pivottabler/vignettes/layout2.png |only pivottabler-1.3.0/pivottabler/vignettes/v00-vignettes.Rmd |only 189 files changed, 3352 insertions(+), 1750 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Dominic Russel [ctb],
Charles F.F Karney [ctb, cph] (Author of included C code from
'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.3.0 dated 2019-12-03 and 0.3.4 dated 2020-02-03
nngeo-0.3.0/nngeo/R/raster_aspect.R |only nngeo-0.3.0/nngeo/R/raster_clump.R |only nngeo-0.3.0/nngeo/R/raster_extend.R |only nngeo-0.3.0/nngeo/R/raster_extract.R |only nngeo-0.3.0/nngeo/R/raster_focal.R |only nngeo-0.3.0/nngeo/R/raster_slope.R |only nngeo-0.3.0/nngeo/R/raster_trim.R |only nngeo-0.3.0/nngeo/man/raster_aspect.Rd |only nngeo-0.3.0/nngeo/man/raster_clump.Rd |only nngeo-0.3.0/nngeo/man/raster_extend.Rd |only nngeo-0.3.0/nngeo/man/raster_extract.Rd |only nngeo-0.3.0/nngeo/man/raster_focal.Rd |only nngeo-0.3.0/nngeo/man/raster_slope.Rd |only nngeo-0.3.0/nngeo/man/raster_trim.Rd |only nngeo-0.3.4/nngeo/DESCRIPTION | 14 +- nngeo-0.3.4/nngeo/LICENSE | 2 nngeo-0.3.4/nngeo/MD5 | 72 ++++++-------- nngeo-0.3.4/nngeo/NAMESPACE | 9 - nngeo-0.3.4/nngeo/NEWS.md | 17 +++ nngeo-0.3.4/nngeo/R/data.R | 27 ++++- nngeo-0.3.4/nngeo/R/focal2.R |only nngeo-0.3.4/nngeo/R/st_connect.R | 93 ++---------------- nngeo-0.3.4/nngeo/R/st_nn.R | 19 ++- nngeo-0.3.4/nngeo/R/st_nn_pnt_geo.R | 1 nngeo-0.3.4/nngeo/R/st_nn_pnt_proj.R | 11 ++ nngeo-0.3.4/nngeo/R/st_nn_poly.R | 1 nngeo-0.3.4/nngeo/R/st_remove_holes.R | 8 + nngeo-0.3.4/nngeo/R/st_segments.R | 14 ++ nngeo-0.3.4/nngeo/R/st_split_junctions.R |only nngeo-0.3.4/nngeo/build/vignette.rds |binary nngeo-0.3.4/nngeo/data/line.RData |only nngeo-0.3.4/nngeo/data/pnt.RData |only nngeo-0.3.4/nngeo/data/towns.RData |binary nngeo-0.3.4/nngeo/inst/doc/intro.R | 25 ++-- nngeo-0.3.4/nngeo/inst/doc/intro.Rmd | 35 +++--- nngeo-0.3.4/nngeo/inst/doc/intro.pdf |binary nngeo-0.3.4/nngeo/man/focal2.Rd |only nngeo-0.3.4/nngeo/man/line.Rd |only nngeo-0.3.4/nngeo/man/nngeo-package.Rd | 3 nngeo-0.3.4/nngeo/man/pnt.Rd |only nngeo-0.3.4/nngeo/man/st_connect.Rd | 9 - nngeo-0.3.4/nngeo/man/st_nn.Rd | 22 ++-- nngeo-0.3.4/nngeo/man/st_segments.Rd | 4 nngeo-0.3.4/nngeo/man/st_split_junctions.Rd |only nngeo-0.3.4/nngeo/man/towns.Rd | 7 - nngeo-0.3.4/nngeo/tests/testthat/test_st_connect.R | 106 ++++++++++----------- nngeo-0.3.4/nngeo/tests/testthat/test_st_nn.R | 32 ++---- nngeo-0.3.4/nngeo/vignettes/intro.Rmd | 35 +++--- 48 files changed, 282 insertions(+), 284 deletions(-)
Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz and other people referred to in the code,
R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-5 dated 2016-10-15 and 1.5-6 dated 2020-02-03
DESCRIPTION | 11 ++++---- INDEX |only MD5 | 13 +++++----- NEWS | 62 +++++++++++++++++++++++++++++--------------------- R/mnormt.R | 4 +-- man/mnormt-package.Rd | 4 +-- src/biv-nt.f | 6 ++-- src/sadmvnt.f | 2 - 8 files changed, 57 insertions(+), 45 deletions(-)
Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>
Diff between ImpactEffectsize versions 0.3.1 dated 2020-01-29 and 0.3.2 dated 2020-02-03
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- R/Impact.R | 7 ++++--- R/plot2Densities.R | 8 ++++---- 5 files changed, 18 insertions(+), 17 deletions(-)
More information about ImpactEffectsize at CRAN
Permanent link
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents.
Functions are provided to let users create tables, modify and format their content.
It extends package 'officer' that does not contain any feature for customized tabular reporting
and can be used within R markdown documents.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.5.6 dated 2019-11-12 and 0.5.7 dated 2020-02-03
flextable-0.5.6/flextable/R/ph_with_flextable.R |only flextable-0.5.7/flextable/DESCRIPTION | 10 flextable-0.5.7/flextable/MD5 | 244 ++++++------ flextable-0.5.7/flextable/NAMESPACE | 4 flextable-0.5.7/flextable/NEWS | 29 + flextable-0.5.7/flextable/R/01_fpstruct.R | 46 +- flextable-0.5.7/flextable/R/05_content.R | 27 + flextable-0.5.7/flextable/R/deprecated.R |only flextable-0.5.7/flextable/R/flextable.R | 8 flextable-0.5.7/flextable/R/flextable_sizes.R | 47 ++ flextable-0.5.7/flextable/R/html_str.R | 3 flextable-0.5.7/flextable/R/merge_flextable.R | 17 flextable-0.5.7/flextable/R/ph_with.R |only flextable-0.5.7/flextable/R/printers.R | 94 ++++ flextable-0.5.7/flextable/R/proc_freq.R | 16 flextable-0.5.7/flextable/R/set_headers.R | 3 flextable-0.5.7/flextable/R/styles.R | 43 +- flextable-0.5.7/flextable/R/tabpart_format.R | 22 - flextable-0.5.7/flextable/R/tabpart_mains.R | 1 flextable-0.5.7/flextable/R/tabpart_tools.R | 50 ++ flextable-0.5.7/flextable/inst/doc/display.R | 26 - flextable-0.5.7/flextable/inst/doc/display.Rmd | 14 flextable-0.5.7/flextable/inst/doc/display.html | 77 +-- flextable-0.5.7/flextable/inst/doc/format.R | 42 -- flextable-0.5.7/flextable/inst/doc/format.Rmd | 29 - flextable-0.5.7/flextable/inst/doc/format.html | 89 +--- flextable-0.5.7/flextable/inst/doc/layout.R | 64 +-- flextable-0.5.7/flextable/inst/doc/layout.html | 90 +--- flextable-0.5.7/flextable/inst/doc/overview.R | 36 + flextable-0.5.7/flextable/inst/doc/overview.Rmd | 14 flextable-0.5.7/flextable/inst/doc/overview.html | 84 +--- flextable-0.5.7/flextable/inst/doc/selectors.R | 18 flextable-0.5.7/flextable/inst/doc/selectors.html | 50 -- flextable-0.5.7/flextable/inst/web_1.0.0/tabwid.css | 24 - flextable-0.5.7/flextable/man/add_header.Rd | 7 flextable-0.5.7/flextable/man/add_header_lines.Rd | 7 flextable-0.5.7/flextable/man/add_header_row.Rd | 13 flextable-0.5.7/flextable/man/align.Rd | 34 + flextable-0.5.7/flextable/man/as_b.Rd | 17 flextable-0.5.7/flextable/man/as_bracket.Rd | 17 flextable-0.5.7/flextable/man/as_chunk.Rd | 17 flextable-0.5.7/flextable/man/as_flextable.Rd | 3 flextable-0.5.7/flextable/man/as_i.Rd | 17 flextable-0.5.7/flextable/man/as_image.Rd | 20 flextable-0.5.7/flextable/man/as_raster.Rd | 18 flextable-0.5.7/flextable/man/as_sub.Rd | 17 flextable-0.5.7/flextable/man/as_sup.Rd | 17 flextable-0.5.7/flextable/man/autofit.Rd | 12 flextable-0.5.7/flextable/man/bg.Rd | 17 flextable-0.5.7/flextable/man/body_add_flextable.Rd | 12 flextable-0.5.7/flextable/man/bold.Rd | 17 flextable-0.5.7/flextable/man/border.Rd | 32 + flextable-0.5.7/flextable/man/border_inner.Rd | 18 flextable-0.5.7/flextable/man/border_inner_h.Rd | 18 flextable-0.5.7/flextable/man/border_inner_v.Rd | 18 flextable-0.5.7/flextable/man/border_outer.Rd | 18 flextable-0.5.7/flextable/man/border_remove.Rd | 18 flextable-0.5.7/flextable/man/borders.Rd | 18 flextable-0.5.7/flextable/man/colformat_char.Rd | 19 flextable-0.5.7/flextable/man/colformat_int.Rd | 20 flextable-0.5.7/flextable/man/colformat_lgl.Rd | 22 - flextable-0.5.7/flextable/man/colformat_num.Rd | 22 - flextable-0.5.7/flextable/man/color.Rd | 17 flextable-0.5.7/flextable/man/compose.Rd | 8 flextable-0.5.7/flextable/man/dim.flextable.Rd | 12 flextable-0.5.7/flextable/man/dim_pretty.Rd | 12 flextable-0.5.7/flextable/man/display.Rd | 11 flextable-0.5.7/flextable/man/docx_value.Rd | 18 flextable-0.5.7/flextable/man/empty_blanks.Rd | 17 flextable-0.5.7/flextable/man/fit_to_width.Rd | 12 flextable-0.5.7/flextable/man/flextable.Rd | 13 flextable-0.5.7/flextable/man/flextable_dim.Rd | 12 flextable-0.5.7/flextable/man/font.Rd | 17 flextable-0.5.7/flextable/man/fontsize.Rd | 17 flextable-0.5.7/flextable/man/footnote.Rd | 3 flextable-0.5.7/flextable/man/format.flextable.Rd | 17 flextable-0.5.7/flextable/man/height.Rd | 12 flextable-0.5.7/flextable/man/hline_bottom.Rd | 18 flextable-0.5.7/flextable/man/hline_top.Rd | 18 flextable-0.5.7/flextable/man/hrule.Rd |only flextable-0.5.7/flextable/man/htmltools_value.Rd | 17 flextable-0.5.7/flextable/man/hyperlink_text.Rd | 21 - flextable-0.5.7/flextable/man/italic.Rd | 17 flextable-0.5.7/flextable/man/knit_print.flextable.Rd | 21 - flextable-0.5.7/flextable/man/linerange.Rd | 34 + flextable-0.5.7/flextable/man/lollipop.Rd | 39 + flextable-0.5.7/flextable/man/merge_at.Rd | 8 flextable-0.5.7/flextable/man/merge_h.Rd | 8 flextable-0.5.7/flextable/man/merge_h_range.Rd | 8 flextable-0.5.7/flextable/man/merge_none.Rd | 8 flextable-0.5.7/flextable/man/merge_v.Rd | 19 flextable-0.5.7/flextable/man/minibar.Rd | 30 + flextable-0.5.7/flextable/man/padding.Rd | 31 + flextable-0.5.7/flextable/man/ph_with.flextable.Rd | 2 flextable-0.5.7/flextable/man/ph_with_flextable.Rd | 4 flextable-0.5.7/flextable/man/plot.flextable.Rd | 17 flextable-0.5.7/flextable/man/print.flextable.Rd | 17 flextable-0.5.7/flextable/man/proc_freq.Rd | 17 flextable-0.5.7/flextable/man/rotate.Rd | 63 ++- flextable-0.5.7/flextable/man/save_as_docx.Rd |only flextable-0.5.7/flextable/man/save_as_html.Rd | 24 - flextable-0.5.7/flextable/man/save_as_image.Rd | 19 flextable-0.5.7/flextable/man/save_as_pptx.Rd |only flextable-0.5.7/flextable/man/set_caption.Rd | 5 flextable-0.5.7/flextable/man/set_formatter.Rd | 13 flextable-0.5.7/flextable/man/set_header_footer_df.Rd | 6 flextable-0.5.7/flextable/man/style.Rd | 11 flextable-0.5.7/flextable/man/theme_alafoli.Rd | 12 flextable-0.5.7/flextable/man/theme_booktabs.Rd | 12 flextable-0.5.7/flextable/man/theme_box.Rd | 13 flextable-0.5.7/flextable/man/theme_tron.Rd | 13 flextable-0.5.7/flextable/man/theme_tron_legacy.Rd | 12 flextable-0.5.7/flextable/man/theme_vader.Rd | 13 flextable-0.5.7/flextable/man/theme_vanilla.Rd | 13 flextable-0.5.7/flextable/man/theme_zebra.Rd | 22 - flextable-0.5.7/flextable/man/valign.Rd | 17 flextable-0.5.7/flextable/man/vline.Rd | 18 flextable-0.5.7/flextable/man/vline_left.Rd | 18 flextable-0.5.7/flextable/man/vline_right.Rd | 18 flextable-0.5.7/flextable/man/width.Rd | 12 flextable-0.5.7/flextable/man/xtable_to_flextable.Rd | 7 flextable-0.5.7/flextable/tests/testthat/test-pptx-tables.R | 4 flextable-0.5.7/flextable/tests/testthat/test-text.R | 2 flextable-0.5.7/flextable/vignettes/display.Rmd | 14 flextable-0.5.7/flextable/vignettes/format.Rmd | 29 - flextable-0.5.7/flextable/vignettes/overview.Rmd | 14 126 files changed, 1738 insertions(+), 1024 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
('Springer', 2009).
Author: Denis Haine [aut, cre] (<https://orcid.org/0000-0002-6691-7335>)
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.9.4 dated 2019-09-02 and 0.9.5 dated 2020-02-03
DESCRIPTION | 12 ++++----- MD5 | 50 ++++++++++++++++++++-------------------- NEWS.md | 3 ++ R/selection.R | 14 +++++------ README.md | 1 build/vignette.rds |binary inst/doc/episensr.R | 46 ++++++++++++++++++------------------ inst/doc/episensr.html | 24 +++++++------------ man/boot.bias.Rd | 3 -- man/confounders.Rd | 9 +++++-- man/confounders.array.Rd | 9 +++++-- man/confounders.emm.Rd | 9 +++++-- man/confounders.evalue.Rd | 10 ++++++-- man/confounders.limit.Rd | 10 ++++++-- man/confounders.poly.Rd | 9 +++++-- man/misclassification.Rd | 9 +++++-- man/misclassification_cov.Rd | 9 +++++-- man/multidimBias.Rd | 15 +++++++++--- man/multiple.bias.Rd | 8 ++++-- man/plot.mbias.Rd | 13 ++++++++-- man/probsens.Rd | 23 ++++++++++++------ man/probsens.conf.Rd | 21 +++++++++++----- man/probsens.irr.Rd | 22 ++++++++++++----- man/probsens.irr.conf.Rd | 21 ++++++++++------ man/probsens.sel.Rd | 27 ++++++++++++--------- tests/testthat/test-selection.R | 14 ++++++++--- 26 files changed, 246 insertions(+), 145 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations. Summarises information about the
tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 0.1-23 dated 2019-07-31 and 0.1-25 dated 2020-02-03
deldir-0.1-23/deldir/src/collincheck.f |only deldir-0.1-23/deldir/src/xsucc.f |only deldir-0.1-25/deldir/ChangeLog | 27 +++++++++++++++++ deldir-0.1-25/deldir/DESCRIPTION | 8 ++--- deldir-0.1-25/deldir/MD5 | 24 +++++++-------- deldir-0.1-25/deldir/data/niProperties.rda |binary deldir-0.1-25/deldir/data/seaweed.rda |binary deldir-0.1-25/deldir/inst/code.discarded/collincheck.f |only deldir-0.1-25/deldir/inst/code.discarded/xsucc.f |only deldir-0.1-25/deldir/inst/ratfor/circen.r | 4 +- deldir-0.1-25/deldir/inst/ratfor/qtest1.r | 11 +++++- deldir-0.1-25/deldir/inst/ratfor/trifnd.r | 6 +++ deldir-0.1-25/deldir/src/circen.f | 4 +- deldir-0.1-25/deldir/src/qtest1.f | 11 +++++- deldir-0.1-25/deldir/src/trifnd.f | 6 +++ 15 files changed, 75 insertions(+), 26 deletions(-)
Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions.
In addition to maximum likelihood regression (for both mean and precision of a beta-distributed
response), bias-corrected and bias-reduced estimation as well as finite mixture models and
recursive partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre],
Francisco Cribari-Neto [aut],
Bettina Gruen [aut],
Ioannis Kosmidis [aut],
Alexandre B. Simas [ctb] (earlier version by),
Andrea V. Rocha [ctb] (earlier version by)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between betareg versions 3.1-2 dated 2019-05-16 and 3.1-3 dated 2020-02-03
DESCRIPTION | 8 - MD5 | 54 ++++++------ NEWS | 6 + build/partial.rdb |binary build/vignette.rds |binary data/CarTask.rda |binary data/FoodExpenditure.rda |binary data/GasolineYield.rda |binary data/ImpreciseTask.rda |binary data/MockJurors.rda |binary data/ReadingSkills.rda |binary data/StressAnxiety.rda |binary data/WeatherTask.rda |binary inst/doc/betareg-ext.R | 2 inst/doc/betareg-ext.Rnw | 2 inst/doc/betareg-ext.pdf |binary inst/doc/betareg.R | 2 inst/doc/betareg.Rnw | 2 inst/doc/betareg.pdf |binary man/GasolineYield.Rd | 2 man/betatree.Rd | 9 +- tests/Examples/betareg-Ex.Rout.save | 64 +++++++------- tests/betatree.R | 7 - tests/betatree.Rout.save | 16 ++- vignettes/betareg-ext.Rnw | 2 vignettes/betareg-ext.Rout.save | 60 ++++++------- vignettes/betareg.Rnw | 2 vignettes/betareg.Rout.save | 159 ++++++++++++++++++------------------ 28 files changed, 209 insertions(+), 188 deletions(-)
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test. The package is based on the publication of Ultsch, A., Thrun, M.C., Hansen-Goos, O., Lotsch, J. (2015) <DOI:10.3390/ijms161025897>.
Author: Michael Thrun [aut, cre] (<https://orcid.org/0000-0001-9542-5543>),
Onno Hansen-Goos [aut, rev],
Rabea Griese [ctr, ctb],
Catharina Lippmann [ctr],
Florian Lerch [ctb, rev],
Jorn Lotsch [dtc, rev, fnd, ctb],
Alfred Ultsch [aut, cph, ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between AdaptGauss versions 1.5.4 dated 2019-11-18 and 1.5.6 dated 2020-02-03
AdaptGauss-1.5.4/AdaptGauss/R/OptimalNoBins.R |only AdaptGauss-1.5.4/AdaptGauss/R/ParetoDensityEstimation.R |only AdaptGauss-1.5.4/AdaptGauss/R/ParetoRadius.R |only AdaptGauss-1.5.4/AdaptGauss/man/OptimalNoBins.Rd |only AdaptGauss-1.5.4/AdaptGauss/man/ParetoDensityEstimation.Rd |only AdaptGauss-1.5.4/AdaptGauss/man/ParetoRadius.Rd |only AdaptGauss-1.5.6/AdaptGauss/DESCRIPTION | 16 AdaptGauss-1.5.6/AdaptGauss/MD5 | 38 - AdaptGauss-1.5.6/AdaptGauss/NAMESPACE | 7 AdaptGauss-1.5.6/AdaptGauss/R/AdaptGauss.R | 8 AdaptGauss-1.5.6/AdaptGauss/R/BayesFor2GMM.R | 294 ++++++------- AdaptGauss-1.5.6/AdaptGauss/R/Chi2testMixtures.R | 6 AdaptGauss-1.5.6/AdaptGauss/R/GMMplot_ggplot2.R |only AdaptGauss-1.5.6/AdaptGauss/R/KStestMixtures.R | 2 AdaptGauss-1.5.6/AdaptGauss/R/LikelihoodRatio4Mixtures.R | 46 +- AdaptGauss-1.5.6/AdaptGauss/R/PlotMixtures.R | 19 AdaptGauss-1.5.6/AdaptGauss/R/RandomLogGMM.R | 12 AdaptGauss-1.5.6/AdaptGauss/build/partial.rdb |binary AdaptGauss-1.5.6/AdaptGauss/inst/doc/AdaptGauss.R | 2 AdaptGauss-1.5.6/AdaptGauss/inst/doc/AdaptGauss.html | 14 AdaptGauss-1.5.6/AdaptGauss/man/AdaptGauss.Rd | 4 AdaptGauss-1.5.6/AdaptGauss/man/GMMplot_ggplot2.Rd |only AdaptGauss-1.5.6/AdaptGauss/man/PlotMixtures.Rd | 5 AdaptGauss-1.5.6/AdaptGauss/man/Symlognpdf.Rd | 3 24 files changed, 252 insertions(+), 224 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-10 2.0
2018-05-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-20 0.2.0.4
2020-01-19 0.2.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-01 0.23.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-21 0.3.3
2020-01-19 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-29 1.0.3
2018-03-19 1.0.2
2018-03-18 1.0.1
2017-11-03 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-07 0.1.1
2019-06-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-19 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-30 0.1.0
Title: Graphical User Interface for FactoMineR
Description: Rcmdr Plugin for the 'FactoMineR' package.
Author: Francois Husson, Julie Josse, Sebastien Le
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between RcmdrPlugin.FactoMineR versions 1.6-0 dated 2016-01-06 and 1.7 dated 2020-02-03
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ R/FactoCA.R | 11 ++++++++++- R/FactoFAMD.R | 11 +++++++++++ R/FactoMCA.R | 35 +++++++++++++++++++++++------------ R/FactoMFA.R | 12 ++++++++++++ R/FactoPCA.R | 13 ++++++++++++- README.md |only 8 files changed, 80 insertions(+), 25 deletions(-)
More information about RcmdrPlugin.FactoMineR at CRAN
Permanent link
Title: Prediction Model Selection and Performance Evaluation in
Multiple Imputed Datasets
Description: Provides functions to apply pooling or backward selection
of logistic, Cox regression and Multilevel (mixed models) prediction
models in multiply imputed datasets. Backward selection can be done
from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and
promising median p-values method. The model can contain
continuous, dichotomous, categorical predictors and interaction terms
between all these type of predictors. Continuous predictors can also
be introduced as restricted cubic spline coefficients. It is also possible
to force (spline) predictors or interaction terms in the model during predictor
selection. The package includes a function to evaluate the stability
of the models using bootstrapping and cluster bootstrapping. The package further
contains functions to generate pooled model performance measures in multiply
imputed datasets as ROC/AUC, R-squares, Brier score, fit test values and
calibration plots for logistic regression models. A function to apply
Bootstrap internal validation is also available where two methods can be
used to combine bootstrapping and multiple imputation. One method, boot_MI,
first draws bootstrap samples and subsequently performs multiple imputation and with
the other method, MI_boot, first bootstrap samples are drawn from each imputed
dataset before results are combined. The adjusted intercept after shrinkage of
the pooled regression coefficients can be subsequently obtained. Backward selection
as part of internal validation is also an option. Also a function to externally
validate logistic prediction models in multiple imputed datasets is available.
Eekhout (2017) <doi:10.1186/s12874-017-0404-7>.
Wiel (2009) <doi:10.1093/biostatistics/kxp011>.
Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut],
Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>
Diff between psfmi versions 0.1.0 dated 2019-05-16 and 0.2.0 dated 2020-02-03
psfmi-0.1.0/psfmi/R/miperform_lr.R |only psfmi-0.1.0/psfmi/man/miperform_lr.Rd |only psfmi-0.2.0/psfmi/DESCRIPTION | 49 psfmi-0.2.0/psfmi/MD5 | 61 psfmi-0.2.0/psfmi/NAMESPACE | 25 psfmi-0.2.0/psfmi/NEWS.md |only psfmi-0.2.0/psfmi/R/D1_cox.R | 10 psfmi-0.2.0/psfmi/R/D1_logistic.R | 10 psfmi-0.2.0/psfmi/R/mivalext_lr.R | 49 psfmi-0.2.0/psfmi/R/pool_intadj.R |only psfmi-0.2.0/psfmi/R/pool_performance.R |only psfmi-0.2.0/psfmi/R/psfmi_D3.R | 2 psfmi-0.2.0/psfmi/R/psfmi_coxr.R | 143 - psfmi-0.2.0/psfmi/R/psfmi_lr.R | 160 - psfmi-0.2.0/psfmi/R/psfmi_mm.R |only psfmi-0.2.0/psfmi/R/psfmi_mm_multiparm.R |only psfmi-0.2.0/psfmi/R/psfmi_perform.R |only psfmi-0.2.0/psfmi/R/psfmi_stab.R |only psfmi-0.2.0/psfmi/README.md | 47 psfmi-0.2.0/psfmi/build/vignette.rds |binary psfmi-0.2.0/psfmi/data/ipdna_md.rda |only psfmi-0.2.0/psfmi/data/lbp_orig.rda |only psfmi-0.2.0/psfmi/data/lbpmilr.rda |binary psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.R | 92 psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.Rmd | 211 + psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.html | 3252 +++++++++++++------------ psfmi-0.2.0/psfmi/man/D1_cox.Rd | 62 psfmi-0.2.0/psfmi/man/D1_logistic.Rd | 60 psfmi-0.2.0/psfmi/man/ipdna_md.Rd |only psfmi-0.2.0/psfmi/man/lbp_orig.Rd |only psfmi-0.2.0/psfmi/man/mivalext_lr.Rd | 195 - psfmi-0.2.0/psfmi/man/pool_intadj.Rd |only psfmi-0.2.0/psfmi/man/pool_performance.Rd |only psfmi-0.2.0/psfmi/man/psfmi_D3.Rd | 72 psfmi-0.2.0/psfmi/man/psfmi_coxr.Rd | 238 - psfmi-0.2.0/psfmi/man/psfmi_lr.Rd | 240 - psfmi-0.2.0/psfmi/man/psfmi_mm.Rd |only psfmi-0.2.0/psfmi/man/psfmi_mm_multiparm.Rd |only psfmi-0.2.0/psfmi/man/psfmi_perform.Rd |only psfmi-0.2.0/psfmi/man/psfmi_stab.Rd |only psfmi-0.2.0/psfmi/vignettes/psfmi-vignette.Rmd | 211 + 41 files changed, 2855 insertions(+), 2334 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates
graphics with details from statistical tests included in the plots
themselves. It is targeted primarily at behavioral sciences community
to provide a one-line code to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports only the most common types of
statistical tests: parametric, nonparametric, robust, and bayesian
versions of t-test/anova, correlation analyses, contingency table
analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>),
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.1.4 dated 2019-12-18 and 0.2.0 dated 2020-02-03
ggstatsplot-0.1.4/ggstatsplot/R/helpers_ggcoefstats_metaanalysis.R |only ggstatsplot-0.1.4/ggstatsplot/man/bf_meta_message.Rd |only ggstatsplot-0.1.4/ggstatsplot/man/ggbetweenstats_switch.Rd |only ggstatsplot-0.1.4/ggstatsplot/man/subtitle_meta_parametric.Rd |only ggstatsplot-0.1.4/ggstatsplot/man/theme_corrmat.Rd |only ggstatsplot-0.1.4/ggstatsplot/man/theme_pie.Rd |only ggstatsplot-0.1.4/ggstatsplot/tests/testthat/test-bf_meta_message.R |only ggstatsplot-0.1.4/ggstatsplot/tests/testthat/test-subtitle_meta_parametric.R |only ggstatsplot-0.2.0/ggstatsplot/DESCRIPTION | 27 ggstatsplot-0.2.0/ggstatsplot/MD5 | 195 +- ggstatsplot-0.2.0/ggstatsplot/NAMESPACE | 27 ggstatsplot-0.2.0/ggstatsplot/NEWS.md | 33 ggstatsplot-0.2.0/ggstatsplot/R/data.R | 30 ggstatsplot-0.2.0/ggstatsplot/R/ggbarstats.R | 22 ggstatsplot-0.2.0/ggstatsplot/R/ggbetweenstats.R | 37 ggstatsplot-0.2.0/ggstatsplot/R/ggcoefstats.R | 295 +--- ggstatsplot-0.2.0/ggstatsplot/R/ggcorrmat.R | 272 +-- ggstatsplot-0.2.0/ggstatsplot/R/gghistostats.R | 80 - ggstatsplot-0.2.0/ggstatsplot/R/ggpiestats.R | 16 ggstatsplot-0.2.0/ggstatsplot/R/ggscatterstats.R | 91 - ggstatsplot-0.2.0/ggstatsplot/R/ggstatsplot-package.R | 8 ggstatsplot-0.2.0/ggstatsplot/R/ggwithinstats.R | 39 ggstatsplot-0.2.0/ggstatsplot/R/grouped_ggbarstats.R | 21 ggstatsplot-0.2.0/ggstatsplot/R/grouped_ggcorrmat.R | 15 ggstatsplot-0.2.0/ggstatsplot/R/grouped_ggpiestats.R | 18 ggstatsplot-0.2.0/ggstatsplot/R/helpers_ggbetweenstats_graphics.R | 31 ggstatsplot-0.2.0/ggstatsplot/R/helpers_ggcoefstats_graphics.R | 118 + ggstatsplot-0.2.0/ggstatsplot/R/helpers_gghistostats_graphics.R | 6 ggstatsplot-0.2.0/ggstatsplot/R/helpers_theme_ggstatsplot.R | 25 ggstatsplot-0.2.0/ggstatsplot/R/reexports.R | 8 ggstatsplot-0.2.0/ggstatsplot/R/switch_functions.R | 106 - ggstatsplot-0.2.0/ggstatsplot/README.md | 58 ggstatsplot-0.2.0/ggstatsplot/build/vignette.rds |binary ggstatsplot-0.2.0/ggstatsplot/data/bugs_wide.rdata |only ggstatsplot-0.2.0/ggstatsplot/inst/CITATION | 2 ggstatsplot-0.2.0/ggstatsplot/inst/WORDLIST | 8 ggstatsplot-0.2.0/ggstatsplot/inst/doc/additional.Rmd | 22 ggstatsplot-0.2.0/ggstatsplot/inst/doc/additional.html | 62 ggstatsplot-0.2.0/ggstatsplot/inst/doc/tests_and_coverage.R |only ggstatsplot-0.2.0/ggstatsplot/inst/doc/tests_and_coverage.Rmd |only ggstatsplot-0.2.0/ggstatsplot/inst/doc/tests_and_coverage.html |only ggstatsplot-0.2.0/ggstatsplot/man/bugs_wide.Rd |only ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggbarstats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggbarstats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggbetweenstats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggbetweenstats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggbetweenstats3-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggcoefstats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggcoefstats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggpiestats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggpiestats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggpiestats3-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggpiestats4-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggscatterstats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggscatterstats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggscatterstats3-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggwithinstats1-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/figures/README-ggwithinstats2-1.png |binary ggstatsplot-0.2.0/ggstatsplot/man/ggbarstats.Rd | 28 ggstatsplot-0.2.0/ggstatsplot/man/ggcoefstats.Rd | 128 - ggstatsplot-0.2.0/ggstatsplot/man/ggcoefstats_label_maker.Rd | 2 ggstatsplot-0.2.0/ggstatsplot/man/ggcorrmat.Rd | 9 ggstatsplot-0.2.0/ggstatsplot/man/ggpiestats.Rd | 27 ggstatsplot-0.2.0/ggstatsplot/man/ggplot_converter.Rd | 3 ggstatsplot-0.2.0/ggstatsplot/man/ggscatterstats.Rd | 4 ggstatsplot-0.2.0/ggstatsplot/man/ggsignif_adder.Rd | 3 ggstatsplot-0.2.0/ggstatsplot/man/ggstatsplot-package.Rd | 8 ggstatsplot-0.2.0/ggstatsplot/man/grouped_ggbarstats.Rd | 29 ggstatsplot-0.2.0/ggstatsplot/man/grouped_ggcorrmat.Rd | 20 ggstatsplot-0.2.0/ggstatsplot/man/grouped_ggpiestats.Rd | 28 ggstatsplot-0.2.0/ggstatsplot/man/histo_labeller.Rd | 3 ggstatsplot-0.2.0/ggstatsplot/man/line_labeller.Rd | 3 ggstatsplot-0.2.0/ggstatsplot/man/parameters_tidy.Rd |only ggstatsplot-0.2.0/ggstatsplot/man/reexports.Rd | 6 ggstatsplot-0.2.0/ggstatsplot/man/theme_ggstatsplot.Rd | 7 ggstatsplot-0.2.0/ggstatsplot/tests/README.md | 379 ++--- ggstatsplot-0.2.0/ggstatsplot/tests/spelling.R | 3 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-argument_count.R | 2 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-combine_plots.R | 6 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggbarstats.R | 40 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 1 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggcoefstats.R | 270 +-- ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggcorrmat.R | 27 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggpiestats.R | 82 - ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggplot_converter.R | 3 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-ggscatterstats.R | 48 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-grouped_ggbarstats.R | 45 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-grouped_ggpiestats.R | 23 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-grouped_ggscatterstats.R | 8 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-helper_messages.R | 3 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-pairwise_ggsignif.R | 33 ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-parameters_tidy.R |only ggstatsplot-0.2.0/ggstatsplot/tests/testthat/test-theme_ggstatsplot.R | 3 ggstatsplot-0.2.0/ggstatsplot/vignettes/additional.Rmd | 22 ggstatsplot-0.2.0/ggstatsplot/vignettes/tests_and_coverage.Rmd |only ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/combine_plots.Rmd | 1 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/gallery.Rmd | 4 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 712 +++++++--- ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 2 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 3 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 91 - ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 4 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 1 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/other_resources.Rmd |only ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 393 ++--- ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/session_info.Rmd | 5 ggstatsplot-0.2.0/ggstatsplot/vignettes/web_only/theme_ggstatsplot.Rmd | 6 107 files changed, 2197 insertions(+), 2003 deletions(-)
Title: Infrastructure for Manipulation Polynomial Matrices
Description: Implementation of class "polyMatrix" for storing a matrix of polynomials and implements
basic matrix operations; including a determinant and characteristic polynomial.
It is based on the package 'polynom' and uses a lot of its methods to implement matrix operations.
This package includes 2 methods of triangularization of polynomial matrices:
Extended Euclidean algorithm which is most classical but numerically unstable;
Sylvester algorithm based on LQ decomposition.
Both methods are described in
D. Henrion & M. Sebek, Reliable numerical methods for polynomial matrix triangularization,
IEEE Transactions on Automatic Control (Volume 44, Issue 3, Mar 1999, Pages 497-508) <doi:10.1109/9.751344>
and in
Salah Labhalla, Henri Lombardi & Roger Marlin,
Algorithmes de calcule de la reduction de Hermite d'une matrice a coefficients polynomeaux,
Theoretical Computer Science (Volume 161, Issue 1-2, July 1996, Pages 69-92) <doi:10.1016/0304-3975(95)00090-9>.
Author: Tamas Prohle [aut],
Peter Prohle [aut],
Nikolai Ryzhkov [aut, cre],
Ildiko Laszlo [aut] (<https://orcid.org/0000-0003-2324-8183>),
Ulas Onat Alakent [ctb]
Maintainer: Nikolai Ryzhkov <namezys@gmail.com>
Diff between polyMatrix versions 0.2.4 dated 2020-01-16 and 0.2.5 dated 2020-02-03
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/const.R | 8 +------- R/dim.R | 13 +++++-------- R/symb.R | 11 ++++------- R/trans.R | 9 +-------- R/triang_euclidean.R | 8 -------- R/triang_sylvester.R | 10 ---------- build/partial.rdb |binary 9 files changed, 24 insertions(+), 61 deletions(-)