Wed, 22 Mar 2017

Package vipor updated to version 0.4.5 with previous version 0.4.4 dated 2016-10-05

Title: Plot Categorical Data Using Quasirandom Noise and Density Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

Diff between vipor versions 0.4.4 dated 2016-10-05 and 0.4.5 dated 2017-03-22

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Package SSDM updated to version 0.2.2 with previous version 0.2.1 dated 2017-03-22

Title: Stacked Species Distribution Modelling
Description: Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.
Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
Maintainer: Sylvain Schmitt <sylvain.schmitt@agroparistech.fr>

Diff between SSDM versions 0.2.1 dated 2017-03-22 and 0.2.2 dated 2017-03-22

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More information about SSDM at CRAN
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Package rtk updated to version 0.2.5 with previous version 0.2.4.1 dated 2017-02-22

Title: Rarefaction Tool Kit
Description: Rarefy data, calculate diversity and plot the results.
Author: Paul Saary, Falk Hildebrand
Maintainer: Paul Saary <rtk@paulsaary.de>

Diff between rtk versions 0.2.4.1 dated 2017-02-22 and 0.2.5 dated 2017-03-22

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More information about rtk at CRAN
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Package readr updated to version 1.1.0 with previous version 1.0.0 dated 2016-08-03

Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Romain Francois [aut], R Core Team [ctb] (Date time code adapted from R), RStudio [cph, fnd], Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jim Hester <james.hester@rstudio.com>

Diff between readr versions 1.0.0 dated 2016-08-03 and 1.1.0 dated 2017-03-22

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More information about readr at CRAN
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Package neuropsychology updated to version 0.5.0 with previous version 0.3.0 dated 2016-11-10

Title: Toolbox for Psychologists, Neuropsychologists and Neuroscientists
Description: Contains statistical functions (for patient assessment, data preprocessing and reporting, ...) and datasets useful in psychology, neuropsychology and neuroscience.
Author: Dominique Makowski [aut, cre], Phillip Alday [ctb]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

Diff between neuropsychology versions 0.3.0 dated 2016-11-10 and 0.5.0 dated 2017-03-22

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More information about neuropsychology at CRAN
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Package KnowBR updated to version 1.2 with previous version 1.1 dated 2017-01-01

Title: Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases
Description: It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.
Author: Cstor Guisande Gonzlez and Jorge M. Lobo
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>

Diff between KnowBR versions 1.1 dated 2017-01-01 and 1.2 dated 2017-03-22

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Package benford.analysis updated to version 0.1.4.1 with previous version 0.1.4 dated 2016-05-08

Title: Benford Analysis for Data Validation and Forensic Analytics
Description: Provides tools that make it easier to validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>

Diff between benford.analysis versions 0.1.4 dated 2016-05-08 and 0.1.4.1 dated 2017-03-22

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Package RWekajars updated to version 3.9.1-2 with previous version 3.9.1-1 dated 2017-01-14

Title: R/Weka Interface Jars
Description: External jars required for package 'RWeka'.
Author: Kurt Hornik [aut, cre], University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package pinnacle.API updated to version 2.0.4 with previous version 1.92 dated 2016-08-10

Title: A Wrapper for the Pinnacle API
Description: An interface to the API by Pinnacle that allows Pinnacle customers to interact with the sports market data in R.See <https://www.pinnacle.com/en/api> for more information. The Pinnacle API can be used to place wagers, retrieve line information, retrieve account information.Please be aware that the TOC of Pinnacle apply <https://www.pinnacle.com/en/termsandconditions>. An account with Pinnacle is necessary to use the Pinnacle API.
Author: Nicholas Jhirad, Marco Blume, Amine Gassem
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>

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More information about pinnacle.API at CRAN
Permanent link

Package pathmapping updated to version 1.0.2 with previous version 1.0.1 dated 2017-03-20

Title: Compute Deviation and Correspondence Between Spatial Paths
Description: Functions to compute and display the area-based deviation between spatial paths and to compute a mapping based on minimizing area and distance-based cost. For details, see: Mueller, S. T., Perelman, B. S., & Veinott, E. S. (2016) <DOI:10.3758/s13428-015-0562-7>.
Author: Shane T. Mueller & Brandon S. Perelman
Maintainer: Shane T. Mueller <shanem@mtu.edu>

Diff between pathmapping versions 1.0.1 dated 2017-03-20 and 1.0.2 dated 2017-03-22

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More information about pathmapping at CRAN
Permanent link

Package OpenMx updated to version 2.7.9 with previous version 2.7.4 dated 2017-01-17

Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others.
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], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph], Stefan Wilhelm [cph], Manjunath B G [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.7.4 dated 2017-01-17 and 2.7.9 dated 2017-03-22

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 OpenMx-2.7.9/OpenMx/DESCRIPTION                                                               |   40 
 OpenMx-2.7.9/OpenMx/MD5                                                                       |  620 +++++-----
 OpenMx-2.7.9/OpenMx/NEWS                                                                      |   20 
 OpenMx-2.7.9/OpenMx/R/0ClassUnion.R                                                           |    4 
 OpenMx-2.7.9/OpenMx/R/MxAlgebra.R                                                             |   12 
 OpenMx-2.7.9/OpenMx/R/MxAlgebraConvert.R                                                      |    4 
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 OpenMx-2.7.9/OpenMx/R/MxCommunication.R                                                       |    1 
 OpenMx-2.7.9/OpenMx/R/MxCompare.R                                                             |   13 
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 OpenMx-2.7.9/OpenMx/R/MxCycleDetection.R                                                      |    2 
 OpenMx-2.7.9/OpenMx/R/MxData.R                                                                |    4 
 OpenMx-2.7.9/OpenMx/R/MxDataWLS.R                                                             |   23 
 OpenMx-2.7.9/OpenMx/R/MxEval.R                                                                |    1 
 OpenMx-2.7.9/OpenMx/R/MxExpectation.R                                                         |   59 
 OpenMx-2.7.9/OpenMx/R/MxExpectationBA81.R                                                     |    6 
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 OpenMx-2.7.9/OpenMx/R/MxExpectationLISREL.R                                                   |   42 
 OpenMx-2.7.9/OpenMx/R/MxExpectationNormal.R                                                   |   42 
 OpenMx-2.7.9/OpenMx/R/MxExpectationRAM.R                                                      |   51 
 OpenMx-2.7.9/OpenMx/R/MxExpectationStateSpace.R                                               |  151 +-
 OpenMx-2.7.9/OpenMx/R/MxFitFunctionML.R                                                       |   13 
 OpenMx-2.7.9/OpenMx/R/MxFitFunctionWLS.R                                                      |    2 
 OpenMx-2.7.9/OpenMx/R/MxModel.R                                                               |    5 
 OpenMx-2.7.9/OpenMx/R/MxNamespace.R                                                           |   11 
 OpenMx-2.7.9/OpenMx/R/MxOptions.R                                                             |   52 
 OpenMx-2.7.9/OpenMx/R/MxPPML.R                                                                |  228 ---
 OpenMx-2.7.9/OpenMx/R/MxReservedNames.R                                                       |    2 
 OpenMx-2.7.9/OpenMx/R/MxRestore.R                                                             |    4 
 OpenMx-2.7.9/OpenMx/R/MxRun.R                                                                 |   22 
 OpenMx-2.7.9/OpenMx/R/MxRunHelperFunctions.R                                                  |    6 
 OpenMx-2.7.9/OpenMx/R/MxSE.R                                                                  |   35 
 OpenMx-2.7.9/OpenMx/R/MxSaturatedModel.R                                                      |    4 
 OpenMx-2.7.9/OpenMx/R/MxSummary.R                                                             |   37 
 OpenMx-2.7.9/OpenMx/R/MxTryHard.R                                                             |    6 
 OpenMx-2.7.9/OpenMx/R/MxVersion.R                                                             |    2 
 OpenMx-2.7.9/OpenMx/R/sysdata.rda                                                             |binary
 OpenMx-2.7.9/OpenMx/README.md                                                                 |   21 
 OpenMx-2.7.9/OpenMx/configure                                                                 |    8 
 OpenMx-2.7.9/OpenMx/inst/CITATION                                                             |    2 
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 OpenMx-2.7.9/OpenMx/inst/models/passing/Acemix2.R                                             |    7 
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 OpenMx-2.7.9/OpenMx/inst/models/passing/Rampart1.R                                            |    4 
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 OpenMx-2.7.9/OpenMx/man/MxBaseNamed-class.Rd                                                  |    3 
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 OpenMx-2.7.9/OpenMx/man/MxFlatModel-class.Rd                                                  |    5 
 OpenMx-2.7.9/OpenMx/man/MxInterval-class.Rd                                                   |    3 
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 OpenMx-2.7.9/OpenMx/man/MxRAMGraph-class.Rd                                                   |    3 
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 OpenMx-2.7.9/OpenMx/man/MxRAMModel-class.Rd                                                   |    3 
 OpenMx-2.7.9/OpenMx/man/OpenMx.Rd                                                             |    1 
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 OpenMx-2.7.9/OpenMx/man/imxAddDependency.Rd                                                   |    1 
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 OpenMx-2.7.9/OpenMx/man/imxConvertLabel.Rd                                                    |    1 
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 OpenMx-2.7.9/OpenMx/man/imxCreateMatrix.Rd                                                    |    3 
 OpenMx-2.7.9/OpenMx/man/imxDataTypes.Rd                                                       |    1 
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 OpenMx-2.7.9/OpenMx/man/imxDeparse.Rd                                                         |    1 
 OpenMx-2.7.9/OpenMx/man/imxDependentModels.Rd                                                 |    1 
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 OpenMx-2.7.9/OpenMx/man/imxDiff.Rd                                                            |    1 
 OpenMx-2.7.9/OpenMx/man/imxDmvnorm.Rd                                                         |    1 
 OpenMx-2.7.9/OpenMx/man/imxEvalByName.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/imxExtractMethod.Rd                                                   |    1 
 OpenMx-2.7.9/OpenMx/man/imxExtractNames.Rd                                                    |    1 
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 OpenMx-2.7.9/OpenMx/man/imxExtractSlot.Rd                                                     |    1 
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 OpenMx-2.7.9/OpenMx/man/imxGenSwift.Rd                                                        |    1 
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 OpenMx-2.7.9/OpenMx/man/imxIdentifier.Rd                                                      |    1 
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 OpenMx-2.7.9/OpenMx/man/imxInitModel.Rd                                                       |    3 
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 OpenMx-2.7.9/OpenMx/man/imxIsPath.Rd                                                          |    1 
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 OpenMx-2.7.9/OpenMx/man/imxLocateIndex.Rd                                                     |    1 
 OpenMx-2.7.9/OpenMx/man/imxLocateLabel.Rd                                                     |    1 
 OpenMx-2.7.9/OpenMx/man/imxLog.Rd                                                             |    1 
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 OpenMx-2.7.9/OpenMx/man/imxModelTypes.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/imxMpiWrap.Rd                                                         |    1 
 OpenMx-2.7.9/OpenMx/man/imxOriginalMx.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/imxPPML.Rd                                                            |    1 
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 OpenMx-2.7.9/OpenMx/man/imxReportProgress.Rd                                                  |    1 
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 OpenMx-2.7.9/OpenMx/man/imxRobustSE.Rd                                                        |    1 
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 OpenMx-2.7.9/OpenMx/man/imxSameType.Rd                                                        |    1 
 OpenMx-2.7.9/OpenMx/man/imxSeparatorChar.Rd                                                   |    1 
 OpenMx-2.7.9/OpenMx/man/imxSfClient.Rd                                                        |    1 
 OpenMx-2.7.9/OpenMx/man/imxSimpleRAMPredicate.Rd                                              |    1 
 OpenMx-2.7.9/OpenMx/man/imxSparseInvert.Rd                                                    |    1 
 OpenMx-2.7.9/OpenMx/man/imxSquareMatrix.Rd                                                    |    1 
 OpenMx-2.7.9/OpenMx/man/imxSymmetricMatrix.Rd                                                 |    1 
 OpenMx-2.7.9/OpenMx/man/imxTypeName.Rd                                                        |    1 
 OpenMx-2.7.9/OpenMx/man/imxUntitledName.Rd                                                    |    1 
 OpenMx-2.7.9/OpenMx/man/imxUntitledNumber.Rd                                                  |    1 
 OpenMx-2.7.9/OpenMx/man/imxUntitledNumberReset.Rd                                             |    1 
 OpenMx-2.7.9/OpenMx/man/imxUpdateModelValues.Rd                                               |    1 
 OpenMx-2.7.9/OpenMx/man/imxVariableTypes.Rd                                                   |    1 
 OpenMx-2.7.9/OpenMx/man/imxVerifyMatrix.Rd                                                    |    1 
 OpenMx-2.7.9/OpenMx/man/imxVerifyModel.Rd                                                     |    1 
 OpenMx-2.7.9/OpenMx/man/imxVerifyName.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/imxVerifyReference.Rd                                                 |    1 
 OpenMx-2.7.9/OpenMx/man/logm.Rd                                                               |    1 
 OpenMx-2.7.9/OpenMx/man/mxAlgebra.Rd                                                          |   13 
 OpenMx-2.7.9/OpenMx/man/mxAlgebraFromString.Rd                                                |    1 
 OpenMx-2.7.9/OpenMx/man/mxAutoStart.Rd                                                        |only
 OpenMx-2.7.9/OpenMx/man/mxAvailableOptimizers.Rd                                              |    1 
 OpenMx-2.7.9/OpenMx/man/mxComputeConfidenceInterval.Rd                                        |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeDefault.Rd                                                   |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeEM.Rd                                                        |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeGradientDescent.Rd                                           |   12 
 OpenMx-2.7.9/OpenMx/man/mxComputeHessianQuality.Rd                                            |    3 
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 OpenMx-2.7.9/OpenMx/man/mxComputeNothing.Rd                                                   |    1 
 OpenMx-2.7.9/OpenMx/man/mxComputeNumericDeriv.Rd                                              |   10 
 OpenMx-2.7.9/OpenMx/man/mxComputeOnce.Rd                                                      |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeReportDeriv.Rd                                               |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeReportExpectation.Rd                                         |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeSequence.Rd                                                  |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeStandardError.Rd                                             |    3 
 OpenMx-2.7.9/OpenMx/man/mxComputeTryHard.Rd                                                   |    3 
 OpenMx-2.7.9/OpenMx/man/mxConstraint.Rd                                                       |    4 
 OpenMx-2.7.9/OpenMx/man/mxDataDynamic.Rd                                                      |    3 
 OpenMx-2.7.9/OpenMx/man/mxEval.Rd                                                             |   11 
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 OpenMx-2.7.9/OpenMx/man/mxGenerateData.Rd                                                     |    3 
 OpenMx-2.7.9/OpenMx/man/mxGetExpected.Rd                                                      |    5 
 OpenMx-2.7.9/OpenMx/man/mxKalmanScores.Rd                                                     |    9 
 OpenMx-2.7.9/OpenMx/man/mxMakeNames.Rd                                                        |    1 
 OpenMx-2.7.9/OpenMx/man/mxNormalQuantiles.Rd                                                  |    1 
 OpenMx-2.7.9/OpenMx/man/mxOption.Rd                                                           |   10 
 OpenMx-2.7.9/OpenMx/man/mxSE.Rd                                                               |   11 
 OpenMx-2.7.9/OpenMx/man/mxSetDefaultOptions.Rd                                                |    1 
 OpenMx-2.7.9/OpenMx/man/mxSimplify2Array.Rd                                                   |    1 
 OpenMx-2.7.9/OpenMx/man/mxTryHard.Rd                                                          |    6 
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 OpenMx-2.7.9/OpenMx/man/omxCheckError.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/omxCheckNamespace.Rd                                                  |    1 
 OpenMx-2.7.9/OpenMx/man/omxCheckWarning.Rd                                                    |    1 
 OpenMx-2.7.9/OpenMx/man/omxConstrainMLThresholds.Rd                                           |    1 
 OpenMx-2.7.9/OpenMx/man/omxDetectCores.Rd                                                     |    1 
 OpenMx-2.7.9/OpenMx/man/omxGetNPSOL.Rd                                                        |    1 
 OpenMx-2.7.9/OpenMx/man/omxGetRAMDepth.Rd                                                     |    1 
 OpenMx-2.7.9/OpenMx/man/omxManifestModelByParameterJacobian.Rd                                |    1 
 OpenMx-2.7.9/OpenMx/man/omxNameAnonymousParameters.Rd                                         |    1 
 OpenMx-2.7.9/OpenMx/man/omxParallelCI.Rd                                                      |    1 
 OpenMx-2.7.9/OpenMx/man/omxQuotes.Rd                                                          |    1 
 OpenMx-2.7.9/OpenMx/man/omxRAMtoML.Rd                                                         |    1 
 OpenMx-2.7.9/OpenMx/man/twinData.Rd                                                           |   11 
 OpenMx-2.7.9/OpenMx/src/AlgebraFunctions.h                                                    |  125 +-
 OpenMx-2.7.9/OpenMx/src/Compute.cpp                                                           |  325 -----
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 OpenMx-2.7.9/OpenMx/src/ComputeGD.cpp                                                         |  415 ++++++
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 OpenMx-2.7.9/OpenMx/src/ComputeNR.cpp                                                         |    6 
 OpenMx-2.7.9/OpenMx/src/ComputeSD.cpp                                                         |   10 
 OpenMx-2.7.9/OpenMx/src/Connectedness.h                                                       |    6 
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 OpenMx-2.7.9/OpenMx/src/autodep                                                               |  199 +--
 OpenMx-2.7.9/OpenMx/src/ba81quad.cpp                                                          |    5 
 OpenMx-2.7.9/OpenMx/src/dmvnorm.cpp                                                           |    5 
 OpenMx-2.7.9/OpenMx/src/finiteDifferences.h                                                   |  259 +++-
 OpenMx-2.7.9/OpenMx/src/fitMultigroup.cpp                                                     |   68 -
 OpenMx-2.7.9/OpenMx/src/fitMultigroup.h                                                       |    2 
 OpenMx-2.7.9/OpenMx/src/glue.cpp                                                              |   23 
 OpenMx-2.7.9/OpenMx/src/glue.h                                                                |   56 
 OpenMx-2.7.9/OpenMx/src/matrix.cpp                                                            |    5 
 OpenMx-2.7.9/OpenMx/src/merge.cpp                                                             |    5 
 OpenMx-2.7.9/OpenMx/src/nloptcpp.cpp                                                          |  150 +-
 OpenMx-2.7.9/OpenMx/src/omxAlgebra.cpp                                                        |   36 
 OpenMx-2.7.9/OpenMx/src/omxAlgebra.h                                                          |    3 
 OpenMx-2.7.9/OpenMx/src/omxAlgebraFitFunction.cpp                                             |   58 
 OpenMx-2.7.9/OpenMx/src/omxData.cpp                                                           |   10 
 OpenMx-2.7.9/OpenMx/src/omxDefines.h                                                          |   72 +
 OpenMx-2.7.9/OpenMx/src/omxExpectation.cpp                                                    |  101 -
 OpenMx-2.7.9/OpenMx/src/omxExpectation.h                                                      |   85 -
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 OpenMx-2.7.9/OpenMx/src/omxExpectationBA81.h                                                  |   11 
 OpenMx-2.7.9/OpenMx/src/omxExportBackendState.cpp                                             |   35 
 OpenMx-2.7.9/OpenMx/src/omxFIMLFitFunction.cpp                                                |  214 +--
 OpenMx-2.7.9/OpenMx/src/omxFIMLFitFunction.h                                                  |  105 +
 OpenMx-2.7.9/OpenMx/src/omxFIMLSingleIteration.cpp                                            |    7 
 OpenMx-2.7.9/OpenMx/src/omxFitFunction.cpp                                                    |  134 --
 OpenMx-2.7.9/OpenMx/src/omxFitFunction.h                                                      |   90 -
 OpenMx-2.7.9/OpenMx/src/omxFitFunctionBA81.cpp                                                |   80 -
 OpenMx-2.7.9/OpenMx/src/omxGREMLExpectation.cpp                                               |   66 -
 OpenMx-2.7.9/OpenMx/src/omxGREMLExpectation.h                                                 |   15 
 OpenMx-2.7.9/OpenMx/src/omxGREMLfitfunction.cpp                                               |  155 +-
 OpenMx-2.7.9/OpenMx/src/omxHessianCalculation.cpp                                             |   13 
 OpenMx-2.7.9/OpenMx/src/omxImportFrontendState.cpp                                            |   26 
 OpenMx-2.7.9/OpenMx/src/omxLISRELExpectation.cpp                                              |   40 
 OpenMx-2.7.9/OpenMx/src/omxLISRELExpectation.h                                                |   13 
 OpenMx-2.7.9/OpenMx/src/omxMLFitFunction.cpp                                                  |   92 -
 OpenMx-2.7.9/OpenMx/src/omxMatrix.cpp                                                         |    8 
 OpenMx-2.7.9/OpenMx/src/omxMatrix.h                                                           |    7 
 OpenMx-2.7.9/OpenMx/src/omxNPSOLSpecific.cpp                                                  |   20 
 OpenMx-2.7.9/OpenMx/src/omxNormalExpectation.cpp                                              |   57 
 OpenMx-2.7.9/OpenMx/src/omxRAMExpectation.cpp                                                 |  248 ++--
 OpenMx-2.7.9/OpenMx/src/omxRFitFunction.cpp                                                   |   28 
 OpenMx-2.7.9/OpenMx/src/omxRFitFunction.h                                                     |   10 
 OpenMx-2.7.9/OpenMx/src/omxRowFitFunction.cpp                                                 |   54 
 OpenMx-2.7.9/OpenMx/src/omxRowFitFunction.h                                                   |    7 
 OpenMx-2.7.9/OpenMx/src/omxSadmvnWrapper.h                                                    |   16 
 OpenMx-2.7.9/OpenMx/src/omxState.cpp                                                          |   32 
 OpenMx-2.7.9/OpenMx/src/omxState.h                                                            |   18 
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 OpenMx-2.7.9/OpenMx/src/omxSymbolTable.cpp                                                    |    7 
 OpenMx-2.7.9/OpenMx/src/omxSymbolTable.h                                                      |    3 
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 OpenMx-2.7.9/OpenMx/src/slsqp.c                                                               |    2 
 OpenMx-2.7.9/OpenMx/src/ssMLFit.cpp                                                           |   76 -
 OpenMx-2.7.9/OpenMx/src/subnp.cpp                                                             |  128 +-
 330 files changed, 4260 insertions(+), 3660 deletions(-)

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Package Biocomb updated to version 0.3 with previous version 0.2 dated 2015-11-27

Title: Feature Selection and Classification with the Embedded Validation Procedures for Biomedical Data Analysis
Description: Contains functions for the data analysis with the emphasis on biological data, including several algorithms for feature ranking, feature selection, classification algorithms with the embedded validation procedures. The functions can deal with numerical as well as with nominal features. Includes also the functions for calculation of feature AUC (Area Under the ROC Curve) and HUM (hypervolume under manifold) values and construction 2D- and 3D- ROC curves. Provides the calculation of Area Above the RCC (AAC) values and construction of Relative Cost Curves (RCC) to estimate the classifier performance under unequal misclassification costs problem. There exists the special function to deal with missing values, including different imputing schemes.
Author: Natalia Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn
Maintainer: Natalia Novoselova <novos65@mail.ru>

Diff between Biocomb versions 0.2 dated 2015-11-27 and 0.3 dated 2017-03-22

 DESCRIPTION             |   18 ++++++-------
 MD5                     |   23 ++++++++--------
 NAMESPACE               |    6 +---
 R/CalculateHUM_ROC.R    |    2 -
 R/CalculateHUM_seq.R    |    2 -
 R/RcppExports.R         |    2 -
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 src/RcppExports.cpp     |   66 ++++++++++++++++++++++++------------------------
 13 files changed, 66 insertions(+), 68 deletions(-)

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Package SSDM updated to version 0.2.1 with previous version 0.2.0 dated 2017-03-17

Title: Stacked Species Distribution Modelling
Description: Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.
Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
Maintainer: Sylvain Schmitt <sylvain.schmitt@agroparistech.fr>

Diff between SSDM versions 0.2.0 dated 2017-03-17 and 0.2.1 dated 2017-03-22

 DESCRIPTION             |    6 
 MD5                     |    8 
 R/gui.R                 |   10 
 README.md               |    2 
 inst/shiny/gui/server.R | 1920 ++++++++++++++++++++++++------------------------
 5 files changed, 976 insertions(+), 970 deletions(-)

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Package rase updated to version 0.3-2 with previous version 0.2-22 dated 2016-01-13

Title: Range Ancestral State Estimation for Phylogeography and Comparative Analyses
Description: Implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015) <DOI:10.1093/sysbio/syv057>. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.
Author: Ignacio Quintero [aut, cre], Forrest W. Crawford [aut], Petr Keil [aut]
Maintainer: Ignacio Quintero <ignacio.quintero@yale.edu>

Diff between rase versions 0.2-22 dated 2016-01-13 and 0.3-2 dated 2017-03-22

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Package randomizeBE updated to version 0.3-3 with previous version 0.3-2 dated 2015-06-30

Title: Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>

Diff between randomizeBE versions 0.3-2 dated 2015-06-30 and 0.3-3 dated 2017-03-22

 DESCRIPTION |   10 +++++-----
 MD5         |    6 +++---
 NEWS        |    4 ++++
 R/RL4_new.R |    2 +-
 4 files changed, 13 insertions(+), 9 deletions(-)

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Package prediction updated to version 0.1.11 with previous version 0.1.10 dated 2017-03-01

Title: Tidy, Type-Safe 'prediction()' Methods
Description: A one-function package containing 'prediction()', a type-safe alternative to 'predict()' that always returns a data frame.
Author: Thomas J. Leeper [aut, cre], Carl Ganz [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between prediction versions 0.1.10 dated 2017-03-01 and 0.1.11 dated 2017-03-22

 DESCRIPTION        |    8 ++++----
 MD5                |    8 ++++----
 NEWS.md            |    4 ++++
 R/build_datalist.R |    6 ++----
 README.md          |   11 +++++++++--
 5 files changed, 23 insertions(+), 14 deletions(-)

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Package oem updated to version 2.0.5 with previous version 2.0.4 dated 2017-02-21

Title: Orthogonalizing EM
Description: Solves penalized least squares problems for big tall data using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut], Jared Huling [aut, cre], Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>

Diff between oem versions 2.0.4 dated 2017-02-21 and 2.0.5 dated 2017-03-22

 DESCRIPTION                 |   10 
 MD5                         |   79 +++----
 NAMESPACE                   |    1 
 R/big_oem.R                 |   66 +++++-
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 README.md                   |  110 ++++++----
 inst/doc/oem_vignette.R     |   51 +++-
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 41 files changed, 3023 insertions(+), 585 deletions(-)

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Package scatterpie updated to version 0.0.7 with previous version 0.0.6 dated 2017-02-14

Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between scatterpie versions 0.0.6 dated 2017-02-14 and 0.0.7 dated 2017-03-22

 DESCRIPTION                   |   17 +++++++++--------
 MD5                           |   22 +++++++++++-----------
 NEWS                          |    6 +++++-
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 build/vignette.rds            |binary
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 12 files changed, 77 insertions(+), 41 deletions(-)

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Package psych updated to version 1.7.3.21 with previous version 1.6.12 dated 2017-01-08

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <http://personality-project.org/r> web page.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>

Diff between psych versions 1.6.12 dated 2017-01-08 and 1.7.3.21 dated 2017-03-22

 DESCRIPTION                   |   15 +
 MD5                           |  127 ++++++++-------
 NAMESPACE                     |   17 +-
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 R/cor.plot.R                  |   36 +---
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 R/esem.R                      |   12 +
 R/fa.R                        |   82 ++++++----
 R/fa.parallel.R               |   43 +++--
 R/factor.stats.R              |  127 ++++++++-------
 R/fisherz.R                   |    5 
 R/fix.dplyr.R                 |only
 R/harmonic.mean.R             |    6 
 R/kappa.R                     |   11 -
 R/mediate.r                   |   22 +-
 R/misc.R                      |  110 ++++++++++++-
 R/multilevel.reliability.R    |only
 R/omegaSem.R                  |    2 
 R/pairs.panels.R              |   26 ++-
 R/plot.irt.R                  |    8 -
 R/print.psych.R               |   61 ++-----
 R/print.psych.omega.R         |   28 ++-
 R/read.clipboard.R            |   41 ++++-
 R/scatter.hist.R              |   39 +++-
 R/score.irt.r                 |    6 
 R/score.items.R               |    2 
 R/scoreOverlap.r              |    2 
 R/set.cor.R                   |   10 -
 R/sim.multilevel.R            |  125 +++++++++++++++
 R/skew.R                      |    3 
 R/statsBy.r                   |   40 +++--
 R/unidim.r                    |only
 build/vignette.rds            |binary
 data/neo.rda                  |binary
 inst/CITATION                 |    8 -
 inst/NEWS.Rd                  |   77 +++++++--
 inst/doc/intro.R              |only
 inst/doc/intro.Rnw            |only
 inst/doc/intro.pdf            |only
 inst/doc/overview.R           |  251 +++++++++----------------------
 inst/doc/overview.Rnw         |  334 ++++++++++++++----------------------------
 inst/doc/overview.pdf         |binary
 inst/doc/psych_for_sem.pdf    |binary
 man/00.psych-package.Rd       |   40 ++---
 man/KMO.Rd                    |   12 -
 man/alpha.Rd                  |    1 
 man/bfi.Rd                    |    2 
 man/cor.plot.Rd               |   19 ++
 man/correct.cor.Rd            |    9 -
 man/dfOrder.Rd                |   12 -
 man/fa.Rd                     |   27 ++-
 man/fa.parallel.Rd            |    3 
 man/fisherz.Rd                |   10 +
 man/harmonic.mean.Rd          |   14 +
 man/kappa.Rd                  |   13 +
 man/mediate.Rd                |   15 +
 man/mssd.Rd                   |   19 ++
 man/multilevel.reliability.Rd |only
 man/omega.Rd                  |    7 
 man/pairs.panels.Rd           |    4 
 man/read.clipboard.Rd         |   54 +++++-
 man/scatter.hist.Rd           |   48 ++++--
 man/score.items.Rd            |    5 
 man/set.cor.Rd                |   17 +-
 man/sim.multilevel.Rd         |   56 ++++++-
 man/tetrachor.Rd              |    6 
 man/unidim.Rd                 |only
 vignettes/intro.Rnw           |only
 vignettes/overview.Rnw        |  334 ++++++++++++++----------------------------
 69 files changed, 1382 insertions(+), 1040 deletions(-)

More information about psych at CRAN
Permanent link

Package polyclip updated to version 1.6-1 with previous version 1.5-6 dated 2016-04-02

Title: Polygon Clipping
Description: R port of Angus Johnson's open source library Clipper. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
Author: Angus Johnson [aut] (C++ original, http://www.angusj.com/delphi/clipper.php), Adrian Baddeley [aut, trl, cre], Brian D. Ripley [ctb], Kurt Hornik [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between polyclip versions 1.5-6 dated 2016-04-02 and 1.6-1 dated 2017-03-22

 DESCRIPTION      |   14 ++++++++------
 MD5              |   11 ++++++-----
 NAMESPACE        |    3 +--
 R/clipper.R      |   15 ++++++++++-----
 configure.ac     |    2 +-
 src/Makevars.win |    1 +
 src/init.c       |only
 7 files changed, 27 insertions(+), 19 deletions(-)

More information about polyclip at CRAN
Permanent link

Package httptest updated to version 1.2.0 with previous version 1.1.0 dated 2017-02-03

Title: A Test Environment for HTTP Requests
Description: Testing code and packages that communicate with remote servers can be painful. Dealing with authentication, bootstrapping server state, cleaning up objects that may get created during the test run, network flakiness, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three test contexts that mock the network connection in different ways, and it offers additional expectations to assert that HTTP requests were--or were not--made. Using these tools, one can test that code is making the intended requests and that it handles the expected responses correctly, all without depending on a connection to a remote API.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>

Diff between httptest versions 1.1.0 dated 2017-02-03 and 1.2.0 dated 2017-03-22

 DESCRIPTION                                 |    8 +--
 MD5                                         |   23 +++++----
 NEWS.md                                     |    8 +++
 R/httptest.R                                |    9 ---
 R/mock-api.R                                |   70 +++++++++++++++++++---------
 R/without-internet.R                        |    9 ++-
 README.md                                   |    2 
 man/buildMockURL.Rd                         |    7 +-
 man/with_mock_API.Rd                        |   19 ++++---
 tests/testthat/api/object1-POST.json        |only
 tests/testthat/api/object1-f913cf-POST.json |only
 tests/testthat/example.com                  |only
 tests/testthat/test-expect-header.R         |    1 
 tests/testthat/test-mock-api.R              |   66 ++++++++++++++++++++++++++
 14 files changed, 164 insertions(+), 58 deletions(-)

More information about httptest at CRAN
Permanent link

Package bWGR updated to version 1.4 with previous version 1.3.2 dated 2016-09-21

Title: Bagging Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, with optional sampling techniques and kernel term.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between bWGR versions 1.3.2 dated 2016-09-21 and 1.4 dated 2017-03-22

 bWGR-1.3.2/bWGR/R/ben.R                |only
 bWGR-1.3.2/bWGR/inst/doc               |only
 bWGR-1.3.2/bWGR/man/ben.Rd             |only
 bWGR-1.3.2/bWGR/src/GSEN.cpp           |only
 bWGR-1.3.2/bWGR/src/KMUP.cpp           |only
 bWGR-1.3.2/bWGR/src/KMUP2.cpp          |only
 bWGR-1.3.2/bWGR/src/emBA.cpp           |only
 bWGR-1.3.2/bWGR/src/emBB.cpp           |only
 bWGR-1.3.2/bWGR/src/emBC.cpp           |only
 bWGR-1.3.2/bWGR/src/emRR.cpp           |only
 bWGR-1.4/bWGR/DESCRIPTION              |   14 ++-
 bWGR-1.4/bWGR/MD5                      |   32 +++-----
 bWGR-1.4/bWGR/NAMESPACE                |    8 +-
 bWGR-1.4/bWGR/R/RcppExports.R          |   36 +++++----
 bWGR-1.4/bWGR/R/wgr.R                  |   74 +++++++++++++++----
 bWGR-1.4/bWGR/inst/CITATION            |   17 ++--
 bWGR-1.4/bWGR/man/bWGR.Rd              |    7 +
 bWGR-1.4/bWGR/man/em.Rd                |   51 +++++++------
 bWGR-1.4/bWGR/man/mkr.Rd               |    6 -
 bWGR-1.4/bWGR/man/wgr.Rd               |   42 ++++++-----
 bWGR-1.4/bWGR/src/Functions.cpp        |only
 bWGR-1.4/bWGR/src/RcppExports.cpp      |  125 +++++++++++++++++++--------------
 bWGR-1.4/bWGR/src/RegisteringDynamic.c |only
 23 files changed, 245 insertions(+), 167 deletions(-)

More information about bWGR at CRAN
Permanent link

Tue, 21 Mar 2017

Package UpSetR updated to version 1.3.3 with previous version 1.3.2 dated 2017-01-04

Title: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.
Author: Jake Conway [cre], Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@hms.harvard.edu>

Diff between UpSetR versions 1.3.2 dated 2017-01-04 and 1.3.3 dated 2017-03-21

 DESCRIPTION         |    6 +++---
 MD5                 |   10 +++++-----
 NEWS                |    8 ++++++++
 R/Element.queries.R |    8 +++++---
 R/MainBar.R         |    4 ++--
 R/Metadata.plots.R  |   32 ++++++++++++++++----------------
 6 files changed, 39 insertions(+), 29 deletions(-)

More information about UpSetR at CRAN
Permanent link

Package stringi updated to version 1.1.3 with previous version 1.1.2 dated 2016-10-01

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 1.1.2 dated 2016-10-01 and 1.1.3 dated 2017-03-21

 stringi-1.1.2/stringi/man/stri_install.Rd                      |only
 stringi-1.1.3/stringi/DESCRIPTION                              |    8 
 stringi-1.1.3/stringi/INSTALL                                  |   30 
 stringi-1.1.3/stringi/LICENSE                                  |    6 
 stringi-1.1.3/stringi/MD5                                      |  367 +++---
 stringi-1.1.3/stringi/NAMESPACE                                |    2 
 stringi-1.1.3/stringi/NEWS                                     |   25 
 stringi-1.1.3/stringi/R/ICU_settings.R                         |    2 
 stringi-1.1.3/stringi/R/compare.R                              |    2 
 stringi-1.1.3/stringi/R/draft_encdetect.R                      |    2 
 stringi-1.1.3/stringi/R/draft_files.R                          |    2 
 stringi-1.1.3/stringi/R/encoding.R                             |    2 
 stringi-1.1.3/stringi/R/encoding_conversion.R                  |    2 
 stringi-1.1.3/stringi/R/encoding_detection.R                   |    2 
 stringi-1.1.3/stringi/R/encoding_management.R                  |    4 
 stringi-1.1.3/stringi/R/escape.R                               |    2 
 stringi-1.1.3/stringi/R/install.R                              |  229 ++--
 stringi-1.1.3/stringi/R/internal_prepare_arg.R                 |    2 
 stringi-1.1.3/stringi/R/internal_test.R                        |    2 
 stringi-1.1.3/stringi/R/join.R                                 |    2 
 stringi-1.1.3/stringi/R/length.R                               |    2 
 stringi-1.1.3/stringi/R/locale.R                               |    2 
 stringi-1.1.3/stringi/R/locale_management.R                    |    2 
 stringi-1.1.3/stringi/R/opts.R                                 |    2 
 stringi-1.1.3/stringi/R/pad.R                                  |    2 
 stringi-1.1.3/stringi/R/random.R                               |    2 
 stringi-1.1.3/stringi/R/reverse.R                              |    2 
 stringi-1.1.3/stringi/R/search.R                               |    2 
 stringi-1.1.3/stringi/R/search_count_4.R                       |    2 
 stringi-1.1.3/stringi/R/search_count_bound.R                   |    2 
 stringi-1.1.3/stringi/R/search_detect_4.R                      |    2 
 stringi-1.1.3/stringi/R/search_extract_4.R                     |    2 
 stringi-1.1.3/stringi/R/search_extract_bound.R                 |    2 
 stringi-1.1.3/stringi/R/search_locate_4.R                      |    2 
 stringi-1.1.3/stringi/R/search_locate_bound.R                  |    2 
 stringi-1.1.3/stringi/R/search_match_4.R                       |    2 
 stringi-1.1.3/stringi/R/search_replace_4.R                     |    2 
 stringi-1.1.3/stringi/R/search_replace_na.R                    |    2 
 stringi-1.1.3/stringi/R/search_split_4.R                       |    2 
 stringi-1.1.3/stringi/R/search_split_bound.R                   |    2 
 stringi-1.1.3/stringi/R/search_startsendswith_4.R              |    2 
 stringi-1.1.3/stringi/R/search_subset_4.R                      |    2 
 stringi-1.1.3/stringi/R/sort.R                                 |    2 
 stringi-1.1.3/stringi/R/stats.R                                |    2 
 stringi-1.1.3/stringi/R/stringi-package.R                      |    4 
 stringi-1.1.3/stringi/R/sub.R                                  |    4 
 stringi-1.1.3/stringi/R/time_calendar.R                        |    2 
 stringi-1.1.3/stringi/R/time_format.R                          |    2 
 stringi-1.1.3/stringi/R/time_symbols.R                         |    2 
 stringi-1.1.3/stringi/R/time_zone.R                            |    2 
 stringi-1.1.3/stringi/R/todo_charclass.R                       |    2 
 stringi-1.1.3/stringi/R/todo_justify.R                         |    2 
 stringi-1.1.3/stringi/R/todo_rbnf.R                            |    2 
 stringi-1.1.3/stringi/R/todo_search_in.R                       |    2 
 stringi-1.1.3/stringi/R/todo_split.R                           |    2 
 stringi-1.1.3/stringi/R/trans_casemap.R                        |    2 
 stringi-1.1.3/stringi/R/trans_normalization.R                  |    2 
 stringi-1.1.3/stringi/R/trans_other.R                          |    2 
 stringi-1.1.3/stringi/R/trans_transliterate.R                  |    2 
 stringi-1.1.3/stringi/R/trim.R                                 |    2 
 stringi-1.1.3/stringi/R/utils.R                                |    2 
 stringi-1.1.3/stringi/R/wrap.R                                 |    2 
 stringi-1.1.3/stringi/configure                                |  162 ++
 stringi-1.1.3/stringi/inst/CITATION                            |    6 
 stringi-1.1.3/stringi/man/stri_enc_set.Rd                      |    2 
 stringi-1.1.3/stringi/man/stri_sub.Rd                          |    2 
 stringi-1.1.3/stringi/man/stringi-package.Rd                   |    2 
 stringi-1.1.3/stringi/src/Makevars.in                          |    3 
 stringi-1.1.3/stringi/src/Makevars.win                         |    2 
 stringi-1.1.3/stringi/src/install.libs.R.in                    |    4 
 stringi-1.1.3/stringi/src/stri_ICU_settings.cpp                |    2 
 stringi-1.1.3/stringi/src/stri_TODO_justify.cpp                |    2 
 stringi-1.1.3/stringi/src/stri_TODO_splitpos.cpp               |    2 
 stringi-1.1.3/stringi/src/stri_TODO_uchar.cpp                  |    2 
 stringi-1.1.3/stringi/src/stri_brkiter.cpp                     |    2 
 stringi-1.1.3/stringi/src/stri_brkiter.h                       |   17 
 stringi-1.1.3/stringi/src/stri_bytesearch_matcher.h            |    2 
 stringi-1.1.3/stringi/src/stri_collator.cpp                    |    2 
 stringi-1.1.3/stringi/src/stri_common.cpp                      |    2 
 stringi-1.1.3/stringi/src/stri_compare.cpp                     |    2 
 stringi-1.1.3/stringi/src/stri_container_base.cpp              |    2 
 stringi-1.1.3/stringi/src/stri_container_base.h                |    2 
 stringi-1.1.3/stringi/src/stri_container_bytesearch.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_container_bytesearch.h          |    2 
 stringi-1.1.3/stringi/src/stri_container_charclass.h           |    2 
 stringi-1.1.3/stringi/src/stri_container_double.h              |    2 
 stringi-1.1.3/stringi/src/stri_container_integer.h             |    2 
 stringi-1.1.3/stringi/src/stri_container_listint.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_container_listint.h             |    2 
 stringi-1.1.3/stringi/src/stri_container_listraw.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_container_listraw.h             |    2 
 stringi-1.1.3/stringi/src/stri_container_listutf8.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_container_listutf8.h            |    2 
 stringi-1.1.3/stringi/src/stri_container_logical.h             |    2 
 stringi-1.1.3/stringi/src/stri_container_regex.cpp             |    2 
 stringi-1.1.3/stringi/src/stri_container_regex.h               |    2 
 stringi-1.1.3/stringi/src/stri_container_usearch.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_container_usearch.h             |    2 
 stringi-1.1.3/stringi/src/stri_container_utf16.cpp             |    2 
 stringi-1.1.3/stringi/src/stri_container_utf16.h               |    2 
 stringi-1.1.3/stringi/src/stri_container_utf8.cpp              |    2 
 stringi-1.1.3/stringi/src/stri_container_utf8.h                |    2 
 stringi-1.1.3/stringi/src/stri_container_utf8_indexable.cpp    |   12 
 stringi-1.1.3/stringi/src/stri_container_utf8_indexable.h      |    2 
 stringi-1.1.3/stringi/src/stri_encoding_conversion.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_encoding_detection.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_encoding_management.cpp         |   10 
 stringi-1.1.3/stringi/src/stri_escape.cpp                      |    2 
 stringi-1.1.3/stringi/src/stri_exception.cpp                   |  548 ++++------
 stringi-1.1.3/stringi/src/stri_exception.h                     |   12 
 stringi-1.1.3/stringi/src/stri_exports.h                       |    2 
 stringi-1.1.3/stringi/src/stri_external.h                      |    8 
 stringi-1.1.3/stringi/src/stri_interval.h                      |    2 
 stringi-1.1.3/stringi/src/stri_intvec.h                        |    2 
 stringi-1.1.3/stringi/src/stri_join.cpp                        |    2 
 stringi-1.1.3/stringi/src/stri_length.cpp                      |    2 
 stringi-1.1.3/stringi/src/stri_macros.h                        |   40 
 stringi-1.1.3/stringi/src/stri_messages.h                      |    2 
 stringi-1.1.3/stringi/src/stri_pad.cpp                         |    2 
 stringi-1.1.3/stringi/src/stri_prepare_arg.cpp                 |    2 
 stringi-1.1.3/stringi/src/stri_random.cpp                      |    2 
 stringi-1.1.3/stringi/src/stri_reverse.cpp                     |    2 
 stringi-1.1.3/stringi/src/stri_search_boundaries_count.cpp     |    2 
 stringi-1.1.3/stringi/src/stri_search_boundaries_extract.cpp   |    2 
 stringi-1.1.3/stringi/src/stri_search_boundaries_locate.cpp    |    2 
 stringi-1.1.3/stringi/src/stri_search_boundaries_split.cpp     |    2 
 stringi-1.1.3/stringi/src/stri_search_class_count.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_class_detect.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_class_extract.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_class_locate.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_class_replace.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_class_split.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_class_startsendswith.cpp |    2 
 stringi-1.1.3/stringi/src/stri_search_class_subset.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_class_trim.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_count.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_detect.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_extract.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_locate.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_replace.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_split.cpp           |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_startsendswith.cpp  |    2 
 stringi-1.1.3/stringi/src/stri_search_coll_subset.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_common.cpp               |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_count.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_detect.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_extract.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_locate.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_replace.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_split.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_startsendswith.cpp |    2 
 stringi-1.1.3/stringi/src/stri_search_fixed_subset.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_in.cpp                   |    2 
 stringi-1.1.3/stringi/src/stri_search_other_replace.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_other_split.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_count.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_detect.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_extract.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_locate.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_match.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_replace.cpp        |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_split.cpp          |    2 
 stringi-1.1.3/stringi/src/stri_search_regex_subset.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_sort.cpp                        |    2 
 stringi-1.1.3/stringi/src/stri_stats.cpp                       |    2 
 stringi-1.1.3/stringi/src/stri_string8.h                       |    2 
 stringi-1.1.3/stringi/src/stri_string8buf.h                    |    2 
 stringi-1.1.3/stringi/src/stri_stringi.cpp                     |    5 
 stringi-1.1.3/stringi/src/stri_stringi.h                       |    2 
 stringi-1.1.3/stringi/src/stri_sub.cpp                         |  138 +-
 stringi-1.1.3/stringi/src/stri_test.cpp                        |    2 
 stringi-1.1.3/stringi/src/stri_time_calendar.cpp               |    2 
 stringi-1.1.3/stringi/src/stri_time_format.cpp                 |    2 
 stringi-1.1.3/stringi/src/stri_time_symbols.cpp                |    2 
 stringi-1.1.3/stringi/src/stri_time_zone.cpp                   |    2 
 stringi-1.1.3/stringi/src/stri_trans_casemap.cpp               |    2 
 stringi-1.1.3/stringi/src/stri_trans_normalization.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_trans_other.cpp                 |    2 
 stringi-1.1.3/stringi/src/stri_trans_transliterate.cpp         |    2 
 stringi-1.1.3/stringi/src/stri_ucnv.cpp                        |    2 
 stringi-1.1.3/stringi/src/stri_ucnv.h                          |    2 
 stringi-1.1.3/stringi/src/stri_uloc.cpp                        |    2 
 stringi-1.1.3/stringi/src/stri_utils.cpp                       |    2 
 stringi-1.1.3/stringi/src/stri_wrap.cpp                        |    2 
 stringi-1.1.3/stringi/src/uconfig_local.h.in                   |    2 
 185 files changed, 1086 insertions(+), 880 deletions(-)

More information about stringi at CRAN
Permanent link

Package rel updated to version 1.3.0 with previous version 1.2.0 dated 2016-12-27

Title: Reliability Coefficients
Description: Derives point estimates with confidence intervals for Bennett et als S, Cohen's kappa, Conger's kappa, Fleiss' kappa, Gwet's AC, intraclass correlation coefficients, Krippendorff's alpha, Scott's pi, the standard error of measurement, and weighted kappa.
Author: Riccardo Lo Martire
Maintainer: Riccardo Lo Martire <Riccardo.Lo.Martire@ki.se>

Diff between rel versions 1.2.0 dated 2016-12-27 and 1.3.0 dated 2017-03-21

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Package qrNLMM updated to version 1.4 with previous version 1.3 dated 2016-06-06

Title: Quantile Regression for Nonlinear Mixed-Effects Models
Description: Quantile regression (QR) for Nonlinear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides graphical summaries for assessing the algorithm convergence and fitting results.
Author: Christian E. Galarza <cgalarza88@gmail.com> and Victor H. Lachos <hlachos@ime.unicamp.br>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

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Package qmethod updated to version 1.5.2 with previous version 1.5 dated 2017-01-24

Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see <http://qmethod.org>). A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors. Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards. The package also offers functions to print Q cards and to generate Q distributions for study administration. The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix. See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author), Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>

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Package censReg updated to version 0.5-26 with previous version 0.5-22 dated 2016-08-20

Title: Censored Regression (Tobit) Models
Description: Maximum Likelihood estimation of censored regression (Tobit) models with cross-sectional and panel data.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

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Package qrLMM updated to version 1.3 with previous version 1.1 dated 2015-01-27

Title: Quantile Regression for Linear Mixed-Effects Models
Description: Quantile regression (QR) for Linear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides graphical summaries for assessing the algorithm convergence and fitting results.
Author: Christian E. Galarza <cgalarza88@gmail.com> and Victor H. Lachos <hlachos@ime.unicamp.br>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

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Package survminer updated to version 0.3.1 with previous version 0.3.0 dated 2017-03-16

Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut], Przemyslaw Biecek [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package frailtypack updated to version 2.11.1 with previous version 2.11.0 dated 2017-03-12

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>

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Package tesseract updated to version 1.4 with previous version 1.3 dated 2016-12-07

Title: Open Source OCR Engine
Description: An OCR engine with unicode (UTF-8) support that can recognize over 100 languages out of the box.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package rsvg updated to version 1.1 with previous version 1.0 dated 2016-08-03

Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size bitmap arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg or webp format. In addition, the package can convert images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package interactionTest updated to version 1.0.1 with previous version 1.0 dated 2015-09-01

Title: Calculates Critical Test Statistics to Control False Discovery and Familywise Error Rates in Marginal Effects Plots
Description: Implements the procedures suggested in Esarey and Sumner (2017) <URL:https://goo.gl/riqX7Q> for controlling the false discovery rate or familywise error rate when constructing marginal effects plots for models with interaction terms.
Author: Justin Esarey and Jane Lawrence Sumner
Maintainer: Justin Esarey <justin@justinesarey.com>

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Package gpg updated to version 0.5 with previous version 0.4 dated 2016-10-30

Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Note that some functionality depends on the version of GnuPG that is installed on the system. On Windows this package can be used together with 'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package WhatIf updated to version 1.5-8 with previous version 1.5-6 dated 2014-01-08

Title: Evaluate Counterfactuals
Description: Inferences about counterfactuals are essential for prediction, answering what if questions, and estimating causal effects. However, when the counterfactuals posed are too far from the data at hand, conclusions drawn from well-specified statistical analyses become based largely on speculation hidden in convenient modeling assumptions that few would be willing to defend. Unfortunately, standard statistical approaches assume the veracity of the model rather than revealing the degree of model-dependence, which makes this problem hard to detect. WhatIf offers easy-to-apply methods to evaluate counterfactuals that do not require sensitivity testing over specified classes of models. If an analysis fails the tests offered here, then we know that substantive inferences will be sensitive to at least some modeling choices that are not based on empirical evidence, no matter what method of inference one chooses to use.
Author: Christopher Gandrud [aut, cre], Gary King [aut], Heather Stoll [aut], Langche Zeng [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>

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Package vardpoor updated to version 0.9.0 with previous version 0.8.6 dated 2017-02-28

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

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Package umx updated to version 1.5.5 with previous version 1.5.1 dated 2017-03-07

Title: Structural Equation Modelling in R with 'OpenMx'
Description: Quickly create, run, and report structural equation and twin models '?umx' to learn more.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>

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Package Rwave updated to version 2.4-5 with previous version 2.4 dated 2015-04-26

Title: Time-Frequency Analysis of 1-D Signals
Description: A set of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.
Author: S original by Rene Carmona <rcarmona@princeton.edu> and Bruno Torresani <bruno.torresani@cmi.univ-mrs.fr>; R port by Brandon Whitcher <bjw34032@users.sourceforge.net>; upgrade by Jonathan M. Lees<jonathan.lees@unc.edu>
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>

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Package rmdformats updated to version 0.3.2 with previous version 0.3.1 dated 2017-02-21

Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra features such as automatic table of contents, lightboxed figures, dynamic crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package questionr updated to version 0.6.0 with previous version 0.5 dated 2016-03-15

Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package pkgconfig updated to version 2.0.1 with previous version 2.0.0 dated 2015-07-18

Title: Private Configuration for 'R' Packages
Description: Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package photobiologyPlants updated to version 0.4.1 with previous version 0.4.0 dated 2016-08-03

Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet (UV) radiation in relation to the photoreceptors Phytochromes, Cryptochromes, and UVR8 which are present in plants. It also includes data sets on the optical properties of plants.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package HRM updated to version 0.5.1 with previous version 0.5.0 dated 2017-02-28

Title: High-Dimensional Repeated Measures
Description: Methods for testing main and interaction effects in possibly high-dimensional repeated measures in factorial designs. The observations of the subjects are assumed to be multivariate normal. It is possible to use up to 2 whole- and 3 subplot factors.
Author: Martin Happ [aut, cre], Harrar W. Solomon [aut], Arne C. Bathke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>

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Package extremefit updated to version 0.2.2 with previous version 0.2.0 dated 2016-12-02

Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
Author: Gilles Durrieu, Ion Grama, Kevin Jaunatre, Quang-Khoai Pham, Jean-Marie Tricot
Maintainer: Kevin Jaunatre <kevin.jaunatre@univ-ubs.fr>

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Package camtrapR updated to version 0.99.8 with previous version 0.99.7 dated 2017-01-31

Title: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre], Alexandre Courtiol [aut], Rahel Sollmann [aut], John Mathai [ctb], Seth Timothy Wong [ctb], An The Truong Nguyen [ctb], Azlan bin Mohamed [ctb], Andrew Tilker [ctb], Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>

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Package bayesImageS updated to version 0.4-0 with previous version 0.3-3 dated 2016-11-03

Title: Bayesian Methods for Image Segmentation using a Potts Model
Description: Various algorithms for segmentation of 2D and 3D images, such as computed tomography and satellite remote sensing. This package implements Bayesian image analysis using the hidden Potts model with external field prior. Latent labels are sampled using chequerboard updating or Swendsen-Wang. Algorithms for the smoothing parameter include pseudolikelihood, path sampling, the exchange algorithm, and approximate Bayesian computation (ABC).
Author: Matt Moores [aut, cre], Kerrie Mengersen [aut], Dai Feng [ctb]
Maintainer: Matt Moores <M.T.Moores@warwick.ac.uk>

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Package anytime updated to version 0.2.2 with previous version 0.2.1 dated 2017-02-09

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between anytime versions 0.2.1 dated 2017-02-09 and 0.2.2 dated 2017-03-21

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Package FactoRizationMachines updated to version 0.11 with previous version 0.1 dated 2016-12-02

Title: Machine Learning with Higher-Order Factorization Machines
Description: Implementation of three machine learning approaches: Support Vector Machines (SVM) with a linear kernel, second-order Factorization Machines (FM), and higher-order Factorization Machines (HoFM).
Author: Julian Knoll
Maintainer: Julian Knoll <julian.knoll@th-nuernberg.de>

Diff between FactoRizationMachines versions 0.1 dated 2016-12-02 and 0.11 dated 2017-03-21

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Package spatstat.utils updated to version 1.4-1 with previous version 1.3-2 dated 2017-02-22

Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.utils versions 1.3-2 dated 2017-02-22 and 1.4-1 dated 2017-03-21

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Package sf updated to version 0.4-0 with previous version 0.3-4 dated 2017-02-06

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection conversions and datum transformations.
Author: Edzer Pebesma [aut, cre], Roger Bivand [ctb], Ian Cook [ctb], Tim Keitt [ctb], Michael Sumner [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb], Etienne Racine [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package ggimage updated to version 0.0.3 with previous version 0.0.2 dated 2017-03-12

Title: Use Image in 'ggplot2'
Description: Supports aesthetic mapping of image files to be visualized in 'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggimage versions 0.0.2 dated 2017-03-12 and 0.0.3 dated 2017-03-21

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Package ergm updated to version 3.7.1 with previous version 3.7.0 dated 2017-03-20

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis.
Author: Mark S. Handcock [aut], David R. Hunter [aut], Carter T. Butts [aut], Steven M. Goodreau [aut], Pavel N. Krivitsky [aut, cre], Martina Morris [aut], Li Wang [ctb], Kirk Li [ctb], Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>

Diff between ergm versions 3.7.0 dated 2017-03-20 and 3.7.1 dated 2017-03-21

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Package TauStar updated to version 1.1.3 with previous version 1.1.0 dated 2016-02-16

Title: Efficient Computation and Testing of the Bergsma-Dassios Sign Covariance
Description: Computes the t* statistic corresponding to the tau* population coefficient introduced by Bergsma and Dassios (2014) <DOI:10.3150/13-BEJ514> and does so in O(n^2) time following the algorithm of Heller and Heller (2016) <https://arxiv.org/abs/1605.08732> building off of the work of Weihs, Drton, and Leung (2016) <DOI:10.1007/s00180-015-0639-x>. Also allows for independence testing using the asymptotic distribution of t* as described by Nandy, Weihs, and Drton (2016) <http://arxiv.org/abs/1602.04387>.
Author: Luca Weihs [aut, cre], Emin Martinian [ctb] (Created the red-black tree library included in package.)
Maintainer: Luca Weihs <lucaw@uw.edu>

Diff between TauStar versions 1.1.0 dated 2016-02-16 and 1.1.3 dated 2017-03-21

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Package SimInf updated to version 4.0.0 with previous version 3.0.0 dated 2017-01-29

Title: A Framework for Data-Driven Stochastic Disease Spread Simulations
Description: Livestock movements are important for the spread of many infectious diseases between herds. The package provides an efficient and flexible framework for stochastic disease spread modelling that integrates within-herd disease dynamics as continuous-time Markov chains and livestock movements between herds as scheduled events. The core simulation solver is implemented in C and uses 'OpenMP' (if available) to divide work over multiple processors. The package contains template models and can be extended with user defined models.
Author: Stefan Widgren (National Veterinary Institute, Sweden), Pavol Bauer (Uppsala University, Sweden), Stefan Engblom (Uppsala University, Sweden)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

Diff between SimInf versions 3.0.0 dated 2017-01-29 and 4.0.0 dated 2017-03-21

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Package RMySQL updated to version 0.10.10 with previous version 0.10.9 dated 2016-05-08

Title: Database Interface and 'MySQL' Driver for R
Description: A 'DBI' interface to 'MySQL' / 'MariaDB'. The CRAN version of this package contains an old branch based on legacy code from S-PLUS, which being phased out. A modern rewrite based on 'Rcpp' can be obtained from the 'Github' repository.
Author: Jeroen Ooms [aut, cre], David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between RMySQL versions 0.10.9 dated 2016-05-08 and 0.10.10 dated 2017-03-21

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Package Rlabkey updated to version 2.1.134 with previous version 2.1.133 dated 2017-01-20

Title: Data Exchange Between R and LabKey Server
Description: The LabKey client library for R makes it easy for R users to load live data from a LabKey Server, <http://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a LabKey Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

Diff between Rlabkey versions 2.1.133 dated 2017-01-20 and 2.1.134 dated 2017-03-21

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Package recosystem updated to version 0.4.1 with previous version 0.4 dated 2016-07-13

Title: Recommender System using Matrix Factorization
Description: R wrapper of the 'libmf' library (http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc. High performance multi-core parallel computing is supported in this package.
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Wei-Sheng Chin, Yong Zhuang, Bo-Wen Yuan, Meng-Yuan Yang, and other contributors. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package RandomFieldsUtils updated to version 0.3.20 with previous version 0.3.15 dated 2016-12-25

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.3.15 dated 2016-12-25 and 0.3.20 dated 2017-03-21

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Package queueing updated to version 0.2.9 with previous version 0.2.8 dated 2016-11-05

Title: Analysis of Queueing Networks and Models
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models and Single and Multiclass Product-Form Queueing Networks. It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K, Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks, Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks and Single Channel Multiple Class Mixed Networks. Also it provides a B-Erlang, C-Erlang and Engset calculators. This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla <pedro.canadilla@gmail.com>

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Package pacotest updated to version 0.2.2 with previous version 0.2.1 dated 2017-03-12

Title: Testing for Partial Copulas and the Simplifying Assumption in Vine Copulas
Description: Routines for two different test types, the Equal Correlation (ECORR) test and the Vectorial Independence (VI) test are provided. The tests can be applied to check whether a conditional copula coincides with its partial copula. Functions to test whether a regular vine copula satisfies the so-called simplifying assumption or to test a single copula within a regular vine copula to be a (j-1)-th order partial copula are available. The ECORR test comes with a decision tree approach to allow testing in high-dimensional settings.
Author: Malte S. Kurz [aut, cre]
Maintainer: Malte S. Kurz <malte.kurz@stat.uni-muenchen.de>

Diff between pacotest versions 0.2.1 dated 2017-03-12 and 0.2.2 dated 2017-03-21

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Package logmult updated to version 0.6.4 with previous version 0.6.3 dated 2016-01-15

Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using gnm, with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre], Heather Turner [ctb], Michael Friendly [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

Diff between logmult versions 0.6.3 dated 2016-01-15 and 0.6.4 dated 2017-03-21

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Package kohonen updated to version 3.0.2 with previous version 3.0.0 dated 2017-03-15

Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

Diff between kohonen versions 3.0.0 dated 2017-03-15 and 3.0.2 dated 2017-03-21

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Package imfr updated to version 0.1.4 with previous version 0.1.3 dated 2017-01-17

Title: Download Data from the International Monetary Fund's Data API
Description: Explore and download data from the International Monetary Fund's data API <http://data.imf.org/>.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

Diff between imfr versions 0.1.3 dated 2017-01-17 and 0.1.4 dated 2017-03-21

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Package highlight updated to version 0.4.7.1 with previous version 0.4.7 dated 2015-04-20

Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
Author: Romain Francois [aut, cre], Andre Simon [ctb]
Maintainer: ORPHANED

Diff between highlight versions 0.4.7 dated 2015-04-20 and 0.4.7.1 dated 2017-03-21

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Package heatmaply updated to version 0.8.2 with previous version 0.7.0 dated 2017-01-22

Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' apps, and available in the 'RStudio' viewer pane, . Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Jonathan Sidi [ctb] (https://github.com/yonicd), Alan Ocallaghan [ctb] (https://github.com/Alanocallaghan), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package gbm updated to version 2.1.3 with previous version 2.1.1 dated 2015-03-11

Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. Includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures (LambdaMart).
Author: Greg Ridgeway <gregridgeway@gmail.com> with contributions from others
Maintainer: ORPHANED

Diff between gbm versions 2.1.1 dated 2015-03-11 and 2.1.3 dated 2017-03-21

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Package ega updated to version 2.0.0 with previous version 1.0.1 dated 2015-02-19

Title: Error Grid Analysis
Description: Functions for assigning Clarke or Parkes (Consensus) error grid zones to blood glucose values, and for plotting both types of error grids in both mg/mL and mmol/L units.
Author: Daniel Schmolze [aut, cre], Sergei Mihhailov [ctb]
Maintainer: Daniel Schmolze <ega@schmolze.com>

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Package effsize updated to version 0.7.1 with previous version 0.7.0 dated 2016-11-14

Title: Efficient Effect Size Computation
Description: A collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano <marco.torchiano@polito.it>

Diff between effsize versions 0.7.0 dated 2016-11-14 and 0.7.1 dated 2017-03-21

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Package earth updated to version 4.4.9.1 with previous version 4.4.9 dated 2017-02-20

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package distory updated to version 1.4.3 with previous version 1.4.2 dated 2013-11-12

Title: Distance Between Phylogenetic Histories
Description: Geodesic distance between phylogenetic trees and associated functions.
Author: John Chakerian and Susan Holmes
Maintainer: ORPHANED

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Package BWStest updated to version 0.2.1 with previous version 0.2.0 dated 2016-04-30

Title: Baumgartner Weiss Schindler Test of Equal Distributions
Description: Performs the 'Baumgartner-Weiss-Schindler' two-sample test of equal probability distributions.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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Package averisk updated to version 1.0.3 with previous version 1.0.2 dated 2016-06-20

Title: Calculation of Average Population Attributable Fractions and Confidence Intervals
Description: Average population attributable fractions are calculated for a set of risk factors (either binary or ordinal valued) for both prospective and case- control designs. Confidence intervals are found by Monte Carlo simulation. The method can be applied to either prospective or case control designs, provided an estimate of disease prevalence is provided. In addition to an exact calculation of AF, an approximate calculation, based on randomly sampling permutations has been implemented to ensure the calculation is computationally tractable when the number of risk factors is large.
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@nuigalway.ie>

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Package addhazard updated to version 1.1.0 with previous version 1.0.0 dated 2015-08-17

Title: Fit Additive Hazards Models for Survival Analysis
Description: Contains tools to fit the additive hazards model to data from a cohort, random sampling, two-phase Bernoulli sampling and two-phase finite population sampling, as well as calibration tool to incorporate phase I auxiliary information into the two-phase data model fitting. This package provides regression parameter estimates and their model-based and robust standard errors. It also offers tools to make prediction of individual specific hazards.
Author: Jie (Kate) Hu [aut, cre], Norman Breslow [aut], Gary Chan [aut]
Maintainer: Jie (Kate) Hu <hujie0704@gmail.com>

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Mon, 20 Mar 2017

Package rbamtools updated to version 2.16.5 with previous version 2.16.4 dated 2017-03-20

Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

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Package photobiologyInOut updated to version 0.4.13 with previous version 0.4.12 dated 2016-10-22

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package photobiology updated to version 0.9.14 with previous version 0.9.13 dated 2016-12-18

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package LW1949 updated to version 1.1.0 with previous version 1.0.0 dated 2015-12-02

Title: An Automated Approach to Evaluating Dose-Effect Experiments Following Litchfield and Wilcoxon (1949)
Description: The manual approach of Litchfield and Wilcoxon (1949) <http://jpet.aspetjournals.org/content/96/2/99.abstract> for evaluating dose-effect experiments is automated so that the computer can do the work.
Author: Jean V. Adams [aut, cre]
Maintainer: Jean V. Adams <jvadams@usgs.gov>

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Package ggspectra updated to version 0.2.1 with previous version 0.2.0 dated 2016-12-22

Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, and statsfor plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and plot() methods for spectral data stored in objects of the classes defined in package 'photobiology' and a plot() method for objects of class "waveband", also defined in package 'photobiology'.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package ggsn updated to version 0.4.0 with previous version 0.3.1 dated 2016-07-06

Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or 'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers to maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>

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Package gfer updated to version 0.1.6 with previous version 0.1.3 dated 2016-12-19

Title: Green Finance and Environmental Risk
Description: Focuses on data collecting and analyzing in green finance and environmental risk research and analysis. Main function includes environmental data collecting from official websites like MEP (Ministry of Environmental Protection of China, <http://www.mep.gov.cn>), water related projects identification and environmental data visualization.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>

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Package europepmc updated to version 0.1.4 with previous version 0.1.3 dated 2017-02-23

Title: R Interface to the Europe PubMed Central RESTful Web Service
Description: An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.
Author: Najko Jahn [aut, cre, cph]
Maintainer: Najko Jahn <najko.jahn@gmail.com>

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Package ks updated to version 1.10.6 with previous version 1.10.5 dated 2017-01-25

Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>

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Package disposables updated to version 1.0.3 with previous version 1.0.1 dated 2015-07-12

Title: Create Disposable R Packages for Testing
Description: Create disposable R packages for testing. You can create, install and load multiple R packages with a single function call, and then unload, uninstall and destroy them with another function call. This is handy when testing how some R code or an R package behaves with respect to other packages.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package TreeSim updated to version 2.3 with previous version 2.2 dated 2015-10-05

Title: Simulating Phylogenetic Trees
Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>

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Package RAC updated to version 1.1.1 with previous version 1.0.1 dated 2016-10-15

Title: R Package for Aqua Culture
Description: Solves the bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass) and shellfish (Mussel and Clam) both at individual and population scale.
Author: Baldan D. [aut, cre], Palazzo D. [ctb], Porporato E.M.D [ctb], Brigolin D. [ctb]
Maintainer: Baldan D. <damiano.baldan91@gmail.com>

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More information about RAC at CRAN
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Package fmsb updated to version 0.6.0 with previous version 0.5.2 dated 2015-09-11

Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
Author: Minato Nakazawa <minato-nakazawa@umin.net>
Maintainer: Minato Nakazawa <minato-nakazawa@umin.net>

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Permanent link

Package astrochron updated to version 0.6.6 with previous version 0.6.5 dated 2016-09-05

Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>

Diff between astrochron versions 0.6.5 dated 2016-09-05 and 0.6.6 dated 2017-03-20

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Permanent link

Package refGenome updated to version 1.7.3 with previous version 1.7.0 dated 2016-05-13

Title: Gene and Splice Site Annotation Using Annotation Data from Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Diff between refGenome versions 1.7.0 dated 2016-05-13 and 1.7.3 dated 2017-03-20

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More information about refGenome at CRAN
Permanent link

Package rbamtools updated to version 2.16.4 with previous version 2.16.0 dated 2016-05-29

Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Diff between rbamtools versions 2.16.0 dated 2016-05-29 and 2.16.4 dated 2017-03-20

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Permanent link

Package rdefra updated to version 0.3.4 with previous version 0.1 dated 2016-06-13

Title: Interact with the UK AIR Pollution Database from DEFRA
Description: Get data from DEFRA's UK-AIR website <https://uk-air.defra.gov.uk/>. It basically scrapes the HTML content.
Author: Claudia Vitolo [aut, cre], Andrew Russell [ctb] (This package is part of the KEHRA project and Andrew supervised the technical/software development.), Allan Tucker [ctb] (This package is part of the KEHRA project and Allan supervised the technical/software development.), Maëlle Salmon [ctb] (Maëlle Salmon reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/68), Hao Zhu [ctb] (Hao Zhu reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/68)
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>

Diff between rdefra versions 0.1 dated 2016-06-13 and 0.3.4 dated 2017-03-20

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Package LNIRT updated to version 0.2.0 with previous version 0.1.0 dated 2016-10-06

Title: LogNormal Response Time Item Response Theory Models
Description: Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports covariates for item and person (random) parameters. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.
Author: Jean-Paul Fox, Rinke Klein Entink, Konrad Klotzke
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>

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Package gRbase updated to version 1.8-3 with previous version 1.8-1 dated 2016-10-16

Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides general features which are used by other graphical modelling packages, in particular by the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' contains several data sets relevant for use in connection with graphical models. Almost all data sets used in the book Graphical Models with R (2012) are contained in 'gRbase'. 'gRbase' implements several graph algorithms (based mainly on representing graphs as adjacency matrices - either in the form of a standard matrix or a sparse matrix). Some graph algorithms are: (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralize. (iii) triangulate. (iv) junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. These features, however, are not maintained anymore and remains in 'gRbase' only because there exists a paper describing these facilities: A Common Platform for Graphical Models in R: The 'gRbase' Package, Journal of Statistical Software, Vol 14, No 17, 2005. NOTICE Proper functionality of 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

Diff between gRbase versions 1.8-1 dated 2016-10-16 and 1.8-3 dated 2017-03-20

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More information about gRbase at CRAN
Permanent link

Package ergm updated to version 3.7.0 with previous version 3.6.1 dated 2017-01-05

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis.
Author: Mark S. Handcock [aut], David R. Hunter [aut], Carter T. Butts [aut], Steven M. Goodreau [aut], Pavel N. Krivitsky [aut, cre], Martina Morris [aut], Li Wang [ctb], Kirk Li [ctb], Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>

Diff between ergm versions 3.6.1 dated 2017-01-05 and 3.7.0 dated 2017-03-20

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Package sticky updated to version 0.5.2 with previous version 0.4.0 dated 2016-11-01

Title: Persist Attributes Across Data Operations
Description: In base R, object attributes are lost when objects are modified by common data operations such as subset, filter, slice, append, extract etc. This packages allows objects to be marked as 'sticky' and have attributes persisted during these operations or when inserted into or extracted from recursive (i.e. list- or table-like) objects.
Author: Christopher Brown [aut, cre], Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>

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Package sadists updated to version 0.2.3 with previous version 0.2.2 dated 2016-03-03

Title: Some Additional Distributions
Description: Provides the density, distribution, quantile and generation functions of some obscure probability distributions, including the doubly non- central t, F, Beta, and Eta distributions; the lambda-prime and K-prime; the upsilon distribution; the (weighted) sum of non-central chi-squares to a power; the (weighted) sum of log non-central chi-squares; the product of non-central chi-squares to powers; the product of doubly non-central F variables; the product of independent normals.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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Package ForestTools updated to version 0.1.2 with previous version 0.1.1 dated 2017-03-06

Title: Analysing Remotely Sensed Forest Data
Description: Forest Tools provides functions for analyzing remotely sensed forest data.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

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Package photobiologyWavebands updated to version 0.4.2 with previous version 0.4.1 dated 2016-08-01

Title: Waveband Definitions for UV, VIS, and IR Radiation
Description: Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package MOEADr updated to version 0.2.1 with previous version 0.2.0 dated 2017-03-16

Title: Component-Wise MOEA/D Implementation
Description: Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals.
Author: Felipe Campelo [aut, cre], Lucas Batista [com], Claus Aranha [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>

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Package evclass updated to version 1.1.1 with previous version 1.1.0 dated 2016-07-01

Title: Evidential Distance-Based Classification
Description: Different evidential distance-based classifiers, which provide outputs in the form of Dempster-Shafer mass functions. The methods are: the evidential K-nearest neighbor rule and the evidential neural network.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>

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