Mon, 31 Aug 2015

Package strvalidator updated to version 1.5.2 with previous version 1.5.0 dated 2015-06-09

Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control. Tools to analyse data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>

Diff between strvalidator versions 1.5.0 dated 2015-06-09 and 1.5.2 dated 2015-08-31

 DESCRIPTION                      |   10 
 MD5                              |  392 +++++++++++++++++++--------------------
 NAMESPACE                        |   46 ++++
 NEWS                             |   34 +++
 R/addColor.r                     |    3 
 R/addData_gui.r                  |    7 
 R/addDye_gui.r                   |    5 
 R/addMarker.r                    |    4 
 R/addMarker_gui.r                |    5 
 R/addSize.r                      |    3 
 R/addSize_gui.r                  |    5 
 R/blockAT.r                      |   11 -
 R/calculateAT.r                  |  146 ++++++++++----
 R/calculateAT6.r                 |   49 +++-
 R/calculateAT6_gui.r             |  110 ++--------
 R/calculateAT_gui.r              |    9 
 R/calculateBalance.r             |    6 
 R/calculateBalance_gui.r         |   12 -
 R/calculateCapillary.r           |    4 
 R/calculateCapillary_gui.r       |    5 
 R/calculateConcordance.r         |    3 
 R/calculateConcordance_gui.r     |    5 
 R/calculateDropout.r             |   10 
 R/calculateDropout_gui.r         |    8 
 R/calculateHeight_gui.r          |    5 
 R/calculateHeterozygous_gui.r    |    5 
 R/calculateMixture_gui.r         |    6 
 R/calculateOL.r                  |    3 
 R/calculateOL_gui.r              |    3 
 R/calculateOverlap.r             |    4 
 R/calculateOverlap_gui.r         |    3 
 R/calculatePeaks.r               |    3 
 R/calculatePeaks_gui.r           |    5 
 R/calculatePullup.r              |    3 
 R/calculatePullup_gui.r          |    7 
 R/calculateResultType.r          |    3 
 R/calculateResultType_gui.r      |    5 
 R/calculateStutter_gui.r         |   10 
 R/checkSubset_gui.r              |    8 
 R/colNames.r                     |    5 
 R/columns.r                      |    3 
 R/columns_gui.r                  |    5 
 R/combine_gui.r                  |    7 
 R/compact.r                      |    3 
 R/cropData_gui.r                 |    5 
 R/editData_gui.r                 |    5 
 R/export.r                       |    5 
 R/export_gui.r                   |    7 
 R/filterProfile.r                |    5 
 R/filterProfile_gui.r            |    8 
 R/generateEPG.r                  |    5 
 R/generateEPG_gui.r              |    5 
 R/getDb.r                        |    3 
 R/getKit.r                       |   25 +-
 R/ggsave_gui.r                   |    6 
 R/guessProfile.r                 |    5 
 R/guessProfile_gui.r             |    2 
 R/heightToPeak.r                 |    5 
 R/import.r                       |   41 +---
 R/import_gui.r                   |    5 
 R/listObjects.r                  |   21 +-
 R/makeKit_gui.r                  |    5 
 R/modelDropout_gui.r             |  106 +++++++---
 R/plotAT_gui.r                   |   12 -
 R/plotBalance_gui.r              |   15 -
 R/plotCapillary_gui.r            |    7 
 R/plotDistribution_gui.r         |   28 +-
 R/plotDropout_gui.r              |   11 -
 R/plotKit_gui.r                  |    6 
 R/plotPeaks_gui.r                |    9 
 R/plotPrecision_gui.r            |   14 -
 R/plotPullup_gui.r               |    8 
 R/plotResultType_gui.r           |   10 
 R/plotStutter_gui.r              |   16 -
 R/slim.r                         |  291 +++++++++++++++++-----------
 R/slim_gui.r                     |    7 
 R/strvalidator.r                 |   11 -
 R/tableBalance.r                 |    5 
 R/tableBalance_gui.r             |    7 
 R/tableCapillary.r               |    7 
 R/tableCapillary_gui.r           |    7 
 R/tablePrecision.r               |    6 
 R/tablePrecision_gui.r           |    8 
 R/tableStutter.r                 |    5 
 R/tableStutter_gui.r             |    7 
 R/trim.r                         |    5 
 R/trim_gui.r                     |    8 
 README.md                        |    9 
 man/addColor.Rd                  |    2 
 man/addData.Rd                   |    2 
 man/addData_gui.Rd               |    2 
 man/addDye_gui.Rd                |    2 
 man/addMarker.Rd                 |    2 
 man/addMarker_gui.Rd             |    2 
 man/addSize.Rd                   |    2 
 man/addSize_gui.Rd               |    2 
 man/blockAT.Rd                   |    5 
 man/calculateAT.Rd               |    9 
 man/calculateAT6.Rd              |    2 
 man/calculateAT6_gui.Rd          |    2 
 man/calculateAT_gui.Rd           |    2 
 man/calculateBalance.Rd          |    4 
 man/calculateBalance_gui.Rd      |    2 
 man/calculateCapillary.Rd        |    2 
 man/calculateCapillary_gui.Rd    |    2 
 man/calculateConcordance.Rd      |    2 
 man/calculateConcordance_gui.Rd  |    2 
 man/calculateDropout.Rd          |    2 
 man/calculateDropout_gui.Rd      |    2 
 man/calculateHeight.Rd           |    2 
 man/calculateHeight_gui.Rd       |    2 
 man/calculateHeterozygous.Rd     |    2 
 man/calculateHeterozygous_gui.Rd |    2 
 man/calculateMixture.Rd          |    2 
 man/calculateMixture_gui.Rd      |    2 
 man/calculateOL.Rd               |    2 
 man/calculateOL_gui.Rd           |    2 
 man/calculateOverlap.Rd          |    2 
 man/calculateOverlap_gui.Rd      |    2 
 man/calculatePeaks.Rd            |    2 
 man/calculatePeaks_gui.Rd        |    2 
 man/calculatePullup.Rd           |    2 
 man/calculatePullup_gui.Rd       |    2 
 man/calculateResultType.Rd       |    2 
 man/calculateResultType_gui.Rd   |    2 
 man/calculateStutter.Rd          |    2 
 man/calculateStutter_gui.Rd      |    2 
 man/checkDataset.Rd              |    2 
 man/checkSubset.Rd               |    2 
 man/checkSubset_gui.Rd           |    2 
 man/colNames.Rd                  |    2 
 man/columns.Rd                   |    2 
 man/columns_gui.Rd               |    2 
 man/combineBinsAndPanels.Rd      |    2 
 man/combine_gui.Rd               |    2 
 man/compact.Rd                   |    2 
 man/cropData_gui.Rd              |    2 
 man/detectKit.Rd                 |    2 
 man/editData_gui.Rd              |    2 
 man/export.Rd                    |    2 
 man/export_gui.Rd                |    2 
 man/filterProfile.Rd             |    2 
 man/filterProfile_gui.Rd         |    2 
 man/generateEPG.Rd               |    2 
 man/generateEPG_gui.Rd           |    2 
 man/getDb.Rd                     |    2 
 man/getKit.Rd                    |    8 
 man/ggsave_gui.Rd                |    2 
 man/guessProfile.Rd              |    2 
 man/guessProfile_gui.Rd          |    2 
 man/heightToPeak.Rd              |    2 
 man/import.Rd                    |    2 
 man/import_gui.Rd                |    2 
 man/listObjects.Rd               |   10 
 man/makeKit_gui.Rd               |    2 
 man/modelDropout_gui.Rd          |   87 ++++++--
 man/plotAT_gui.Rd                |    2 
 man/plotBalance_gui.Rd           |    2 
 man/plotCapillary_gui.Rd         |    2 
 man/plotDistribution_gui.Rd      |    2 
 man/plotDropout_gui.Rd           |    2 
 man/plotKit_gui.Rd               |    2 
 man/plotPeaks_gui.Rd             |    2 
 man/plotPrecision_gui.Rd         |    2 
 man/plotPullup_gui.Rd            |    2 
 man/plotResultType_gui.Rd        |    2 
 man/plotStutter_gui.Rd           |    2 
 man/readBinsFile.Rd              |    2 
 man/readPanelsFile.Rd            |    2 
 man/ref1.Rd                      |    2 
 man/ref11.Rd                     |    2 
 man/ref2.Rd                      |    2 
 man/ref3.Rd                      |    2 
 man/ref4.Rd                      |    2 
 man/ref51.Rd                     |    2 
 man/ref52.Rd                     |    2 
 man/saveObject.Rd                |    2 
 man/set1.Rd                      |    2 
 man/set2.Rd                      |    2 
 man/set3.Rd                      |    2 
 man/set4.Rd                      |    2 
 man/set5.Rd                      |    2 
 man/slim.Rd                      |    2 
 man/slim_gui.Rd                  |    2 
 man/sortMarker.Rd                |    2 
 man/strValidator-package.Rd      |    2 
 man/strvalidator.Rd              |    4 
 man/tableBalance.Rd              |    2 
 man/tableBalance_gui.Rd          |    2 
 man/tableCapillary.Rd            |    2 
 man/tableCapillary_gui.Rd        |    2 
 man/tablePrecision.Rd            |    2 
 man/tablePrecision_gui.Rd        |    2 
 man/tableStutter.Rd              |    2 
 man/tableStutter_gui.Rd          |    2 
 man/trim.Rd                      |    2 
 man/trim_gui.Rd                  |    2 
 197 files changed, 1300 insertions(+), 807 deletions(-)

More information about strvalidator at CRAN
Permanent link

Package ridigbio updated to version 0.3.1 with previous version 0.3 dated 2015-07-14

Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph], Matthew Collins [aut, cre], Scott Chamberlain [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>

Diff between ridigbio versions 0.3 dated 2015-07-14 and 0.3.1 dated 2015-08-31

 DESCRIPTION                             |    8 +++---
 MD5                                     |    6 ++---
 tests/testthat/test-idig_count_media.R  |   38 ++++++++++++++++----------------
 tests/testthat/test-idig_search_media.R |    2 -
 4 files changed, 27 insertions(+), 27 deletions(-)

More information about ridigbio at CRAN
Permanent link

Package MixAll updated to version 1.1.1 with previous version 1.0.2 dated 2015-04-04

Title: Clustering using Mixture Models
Description: Algorithms and methods for estimating parametric mixture models with missing data.
Author: Serge Iovleff [aut, cre]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>

Diff between MixAll versions 1.0.2 dated 2015-04-04 and 1.1.1 dated 2015-08-31

 DESCRIPTION                               |   16 -
 MD5                                       |  155 ++++++-----
 NAMESPACE                                 |   11 
 R/ClusterAlgo.R                           |   47 ++-
 R/ClusterCategorical.R                    |   34 +-
 R/ClusterDiagGaussian.R                   |   32 +-
 R/ClusterGamma.R                          |   28 +-
 R/ClusterHeterogeneous.R                  |    8 
 R/ClusterInit.R                           |   44 ++-
 R/ClusterKernel.R                         |only
 R/ClusterModelNames.R                     |  162 ++++++++---
 R/ClusterPoisson.R                        |    5 
 R/ClusterStrategy.R                       |    8 
 R/IClusterModel.R                         |    2 
 R/MixAll.R                                |   29 +-
 R/global.R                                |   13 
 R/missingValues.R                         |   18 +
 build/vignette.rds                        |binary
 data/bullsEye.rda                         |only
 inst/doc/Introduction-Mixtures.R          |   57 ++--
 inst/doc/Introduction-Mixtures.Rnw        |  406 +++++++++++++++++++++---------
 inst/doc/Introduction-Mixtures.pdf        |binary
 man/ClusterAlgo-class.Rd                  |    8 
 man/ClusterCategorical-class.Rd           |    4 
 man/ClusterCategoricalComponent-class.Rd  |    6 
 man/ClusterDiagGaussian-class.Rd          |    2 
 man/ClusterDiagGaussianComponent-class.Rd |    4 
 man/ClusterGamma-class.Rd                 |    6 
 man/ClusterGammaComponent-class.Rd        |    6 
 man/ClusterHeterogeneous-class.Rd         |    2 
 man/ClusterInit-class.Rd                  |    2 
 man/ClusterKernel-class.Rd                |only
 man/ClusterKernelComponent-class.Rd       |only
 man/ClusterModels-class.Rd                |    2 
 man/ClusterPoisson-class.Rd               |    2 
 man/ClusterStrategy-class.Rd              |    2 
 man/DebTrivedi.Rd                         |    2 
 man/HeartDisease.Rd                       |    2 
 man/IClusterComponent-class.Rd            |    2 
 man/MixAll-package.Rd                     |   18 -
 man/birds.Rd                              |    2 
 man/bullsEye.Rd                           |only
 man/car.Rd                                |    2 
 man/clusterAlgo.Rd                        |   13 
 man/clusterCategorical.Rd                 |   23 -
 man/clusterCategoricalNames.Rd            |    9 
 man/clusterDiagGaussian.Rd                |   16 -
 man/clusterDiagGaussianNames.Rd           |   28 +-
 man/clusterGamma.Rd                       |   13 
 man/clusterGammaNames.Rd                  |   23 -
 man/clusterHeterogeneous.Rd               |    6 
 man/clusterInit.Rd                        |    5 
 man/clusterKernel.Rd                      |only
 man/clusterKernelNames.Rd                 |only
 man/clusterPoisson.Rd                     |    4 
 man/clusterPoissonNames.Rd                |    9 
 man/clusterStrategy.Rd                    |    2 
 man/extract-methods.Rd                    |    7 
 man/geyser.Rd                             |    2 
 man/initialize-methods.Rd                 |   21 +
 man/missingValues-methods.Rd              |   19 +
 man/plot-ClusterCategorical-method.Rd     |    4 
 man/plot-ClusterDiagGaussian-method.Rd    |    4 
 man/plot-ClusterGamma-method.Rd           |    4 
 man/plot-ClusterHeterogeneous-method.Rd   |    2 
 man/plot-ClusterKernel-method.Rd          |only
 man/plot-ClusterPoisson-method.Rd         |    4 
 man/print-methods.Rd                      |   10 
 man/show-methods.Rd                       |   12 
 man/summary-methods.Rd                    |    7 
 man/titanic.Rd                            |    2 
 src/ClusterFacade.cpp                     |   23 -
 src/ClusterFacade.h                       |    4 
 src/ClusterLauncher.cpp                   |  151 +++++++----
 src/ClusterLauncher.h                     |   41 ++-
 src/RDataHandler.cpp                      |    5 
 src/RDataHandler.h                        |   24 -
 src/RankMixture                           |only
 src/clusterMixture.cpp                    |   76 +++++
 tests/simulHeterogeneous.R                |only
 vignettes/Introduction-Mixtures.Rnw       |  406 +++++++++++++++++++++---------
 vignettes/MixAll.bib                      |   26 +
 82 files changed, 1460 insertions(+), 694 deletions(-)

More information about MixAll at CRAN
Permanent link

Package copBasic updated to version 2.0.1 with previous version 1.7.1 dated 2015-01-30

Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related mathematical operations oriented around the oft cited and fundamental bicopula theory described by Nelsen (2006), Joe (2014), and other selected works. The lower, upper, product, and a few select other bicopula are implemented. Individual copula support is deliberately limited to keep the package focused on an educational API to major bicopula theory. Expressions for an arbitrary bicopula include the diagonal, survival copula, the dual of a copula, co-copula, and numerical bicopula density. Level curves (sets) as well as horizontal and vertical sections and derivatives of such sections also are supported. The numerical derivatives of a bicopula are provided as well as inverses; simulation by the conditional distribution method thus are supported. Composition, convex combination, and products of bicopula are provided. Copula properties include Kendall Function and L-moments thereof, Kendall Tau, Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-Wolff Sigma, tail dependency and order, and skewness. Evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing are available. Kullback-Leibler divergence, Vuong's procedure, and L-comoments for copula inference are available. Quantile and median regressions for V with respect to U and U with respect to V are available. Empirical copulas (EC) are supported.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>

Diff between copBasic versions 1.7.1 dated 2015-01-30 and 2.0.1 dated 2015-08-31

 ChangeLog                                   |  125 ++++++++++--
 DESCRIPTION                                 |   12 -
 MD5                                         |  273 ++++++++++++++++------------
 NAMESPACE                                   |   41 +++-
 R/COP.R                                     |   21 +-
 R/COPinv.R                                  |   20 +-
 R/COPinv2.R                                 |   18 +
 R/EMPIRcop.R                                |   69 +++----
 R/EMPIRsim.R                                |   54 ++++-
 R/FRECHETcop.R                              |   17 -
 R/GHcop.R                                   |   40 +++-
 R/GLcop.R                                   |only
 R/HRcop.R                                   |only
 R/P.R                                       |    2 
 R/PARETOcop.R                               |only
 R/PSP.R                                     |    8 
 R/W.R                                       |    2 
 R/blomCOP.R                                 |    6 
 R/composite1COP.R                           |    4 
 R/composite2COP.R                           |    5 
 R/composite3COP.R                           |    3 
 R/convex2COP.R                              |only
 R/copBasic.fitpara.R                        |only
 R/densityCOP.R                              |   25 +-
 R/derCOPinv.R                               |    9 
 R/derCOPinv2.R                              |    9 
 R/diagCOPatf.R                              |   46 +++-
 R/footCOP.R                                 |only
 R/giniCOP.R                                 |   24 ++
 R/hoefCOP.R                                 |   93 +++++++--
 R/isfuncCOP.R                               |only
 R/joeskewCOP.R                              |only
 R/joint.curvesCOP.R                         |only
 R/joint.curvesCOP2.R                        |only
 R/jointCOP.R                                |only
 R/kfuncCOP.R                                |only
 R/kfuncCOPinv.R                             |only
 R/kfuncCOPlmoms.R                           |only
 R/kullCOP.R                                 |  102 +++++++++-
 R/lcomCOPpv.R                               |  132 +++++++------
 R/prod2COP.R                                |only
 R/qua.regressCOP.draw.R                     |    8 
 R/rhoCOP.R                                  |   22 +-
 R/rhobevCOP.R                               |only
 R/semicorCOP.R                              |   12 -
 R/simCOP.R                                  |   12 -
 R/simCOPmicro.R                             |   20 +-
 R/statTn.R                                  |only
 R/tailconCOP.R                              |only
 R/tauCOP.R                                  |   73 +++++--
 R/uvlmoms.R                                 |   10 -
 R/vuongCOP.R                                |   79 ++++++--
 R/wolfCOP.R                                 |   45 +++-
 inst/CITATION                               |    2 
 inst/doc/CopulaRelations_BaseFigure_inR.txt |only
 man/COP.Rd                                  |   43 ++++
 man/COPinv.Rd                               |   13 +
 man/COPinv2.Rd                              |   13 +
 man/EMPIRcop.Rd                             |  143 ++++++++++----
 man/EMPIRcopdf.Rd                           |    5 
 man/EMPIRgrid.Rd                            |    4 
 man/EMPIRgridder.Rd                         |    2 
 man/EMPIRgridder2.Rd                        |    2 
 man/EMPIRgridderinv.Rd                      |    2 
 man/EMPIRgridderinv2.Rd                     |    2 
 man/EMPIRmed.regress.Rd                     |    2 
 man/EMPIRmed.regress2.Rd                    |    2 
 man/EMPIRqua.regress.Rd                     |    4 
 man/EMPIRqua.regress2.Rd                    |    4 
 man/EMPIRsim.Rd                             |   39 +++-
 man/EMPIRsimv.Rd                            |   35 +--
 man/FRECHETcop.Rd                           |   44 +++-
 man/GHcop.Rd                                |  236 ++++++++++++++++++++----
 man/GLcop.Rd                                |only
 man/HRcop.Rd                                |only
 man/M.Rd                                    |    3 
 man/N4212cop.Rd                             |   15 -
 man/P.Rd                                    |    8 
 man/PARETOcop.Rd                            |only
 man/PLACKETTcop.Rd                          |   23 +-
 man/PLACKETTpar.Rd                          |   40 ++--
 man/PLACKETTsim.Rd                          |    4 
 man/PSP.Rd                                  |    8 
 man/PlackettPlackettABKGtest.Rd             |   20 +-
 man/PlackettPlackettNP.Rd                   |   16 -
 man/ReineckeWell266.Rd                      |    3 
 man/ReineckeWells.Rd                        |    3 
 man/W.Rd                                    |    3 
 man/asCOP.Rd                                |   12 -
 man/blomCOP.Rd                              |   28 +-
 man/coCOP.Rd                                |   17 +
 man/composite1COP.Rd                        |    6 
 man/composite2COP.Rd                        |   12 -
 man/composite3COP.Rd                        |   18 +
 man/convex2COP.Rd                           |only
 man/copBasic-package.Rd                     |  174 +++++++++++------
 man/copBasic.fitpara.Rd                     |only
 man/densityCOP.Rd                           |   21 +-
 man/densityCOPplot.Rd                       |   28 +-
 man/derCOP.Rd                               |   23 +-
 man/derCOP2.Rd                              |   18 -
 man/derCOPinv.Rd                            |  121 ++++++++++--
 man/derCOPinv2.Rd                           |   42 ++--
 man/diagCOP.Rd                              |   21 +-
 man/diagCOPatf.Rd                           |   40 ++--
 man/duCOP.Rd                                |   93 ++++++++-
 man/figures                                 |only
 man/footCOP.Rd                              |only
 man/giniCOP.Rd                              |   88 ++++++---
 man/gridCOP.Rd                              |   17 +
 man/hoefCOP.Rd                              |  102 +++++++---
 man/isCOP.LTD.Rd                            |    6 
 man/isCOP.PQD.Rd                            |   56 +++--
 man/isCOP.RTI.Rd                            |    9 
 man/isCOP.permsym.Rd                        |   10 -
 man/isCOP.radsym.Rd                         |   34 +--
 man/isfuncCOP.Rd                            |only
 man/joeskewCOP.Rd                           |only
 man/joint.curvesCOP.Rd                      |only
 man/joint.curvesCOP2.Rd                     |only
 man/jointCOP.Rd                             |only
 man/kfuncCOP.Rd                             |only
 man/kfuncCOPinv.Rd                          |only
 man/kfuncCOPlmoms.Rd                        |only
 man/kullCOP.Rd                              |   93 +++++----
 man/lcomCOPpv.Rd                            |   24 +-
 man/lcomoms2.ABKGcop2parameter.Rd           |   13 -
 man/lcomoms2.ABcop2parameter.Rd             |   20 --
 man/level.curvesCOP.Rd                      |   25 +-
 man/level.curvesCOP2.Rd                     |   15 -
 man/level.setCOP.Rd                         |   13 -
 man/level.setCOP2.Rd                        |   16 -
 man/med.regressCOP.Rd                       |   21 --
 man/med.regressCOP2.Rd                      |    9 
 man/prod2COP.Rd                             |only
 man/qua.regressCOP.Rd                       |   27 +-
 man/qua.regressCOP.draw.Rd                  |    6 
 man/qua.regressCOP2.Rd                      |    4 
 man/rhoCOP.Rd                               |   25 +-
 man/rhobevCOP.Rd                            |only
 man/sectionCOP.Rd                           |   15 -
 man/semicorCOP.Rd                           |   29 +-
 man/simCOP.Rd                               |   29 +-
 man/simCOPmicro.Rd                          |   82 ++++++++
 man/simcomposite3COP.Rd                     |   13 -
 man/simcompositeCOP.Rd                      |   21 --
 man/statTn.Rd                               |only
 man/surCOP.Rd                               |   13 -
 man/surfuncCOP.Rd                           |   14 +
 man/tailconCOP.Rd                           |only
 man/taildepCOP.Rd                           |   54 +++--
 man/tailordCOP.Rd                           |   34 +--
 man/tauCOP.Rd                               |   65 ++++--
 man/uvlmoms.Rd                              |   40 ++--
 man/vuongCOP.Rd                             |  165 +++++++++-------
 man/wolfCOP.Rd                              |   44 +++-
 156 files changed, 2754 insertions(+), 1355 deletions(-)

More information about copBasic at CRAN
Permanent link

Package BDgraph updated to version 2.22 with previous version 2.21 dated 2015-08-23

Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Bayesian inference for structure learning in undirected graphical models. The main target is to uncover complicated patterns in multivariate data wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>

Diff between BDgraph versions 2.21 dated 2015-08-23 and 2.22 dated 2015-08-31

 DESCRIPTION            |    8 +-
 MD5                    |   24 +++----
 NAMESPACE              |    1 
 R/bdgraph.R            |  124 ++++++++++++++++++++------------------
 R/plotcoda.R           |    5 -
 R/select.R             |    2 
 R/traceplot.R          |   57 +++++++++--------
 build/vignette.rds     |binary
 man/BDgraph-package.Rd |    2 
 man/bdgraph.Rd         |   15 +---
 man/plotcoda.Rd        |    2 
 man/traceplot.Rd       |    4 -
 src/BDgraph.cpp        |  157 +++++++++++++++++++++++++++----------------------
 13 files changed, 214 insertions(+), 187 deletions(-)

More information about BDgraph at CRAN
Permanent link

Package apt updated to version 2.4 with previous version 2.3 dated 2014-11-27

Title: Asymmetric Price Transmission
Description: Asymmetric price transmission between two time series is assessed. Several functions are available for linear and nonlinear threshold cointegration, and furthermore, symmetric and asymmetric error correction model. A graphical user interface is also included for major functions included in the package, so users can also use these functions in a more intuitive way.
Author: Changyou Sun <cs258@msstate.edu>
Maintainer: Changyou Sun <cs258@msstate.edu>

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Package RGA updated to version 0.2.4 with previous version 0.2.3 dated 2015-07-27

Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>

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Package PrevMap updated to version 1.2.2 with previous version 1.2.1 dated 2015-08-13

Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data, and is also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>

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Package hglm updated to version 2.1-1 with previous version 2.1-0 dated 2015-05-19

Title: Hierarchical Generalized Linear Models
Description: Procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Moudud Alam, Lars Ronnegard, Xia Shen
Maintainer: Xia Shen <xia.shen@ki.se>

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Package ChainLadder updated to version 0.2.2 with previous version 0.2.1 dated 2015-07-11

Title: Statistical Methods and Models for Claims Reserving in General Insurance
Description: Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.
Author: Markus Gesmann [aut, cre], Daniel Murphy [aut], Yanwei (Wayne) Zhang [aut], Alessandro Carrato [aut], Giuseppe Crupi [aut], Christophe Dutang [ctb], Arnaud Lacoume [ctb], Arthur Charpentier [ctb], Mario Wuthrich [aut], Fabio Concina [aut]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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Package ZRA updated to version 0.2 with previous version 0.1 dated 2015-08-23

Title: Dynamic Plots for Time Series Forecasting
Description: Combines a forecast of a time series, using the function forecast(), with the dynamic plots from dygraphs.
Author: David Beiner
Maintainer: David Beiner <zra.r.package@gmail.com>

Diff between ZRA versions 0.1 dated 2015-08-23 and 0.2 dated 2015-08-31

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Package urltools updated to version 1.2.1 with previous version 1.2.0 dated 2015-06-19

Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL encoding and decoding, parsing, and parameter extraction. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb], Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>

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Package soc.ca updated to version 0.7.2 with previous version 0.7.1 dated 2014-02-08

Title: Specific Correspondence Analysis for the Social Sciences
Description: Specific and class specific multiple correspondence analysis on survey-like data. Soc.ca is optimized to the needs of the social scientist and presents easily interpretable results in near publication ready quality.
Author: Anton Grau Larsen, with contributions from Christoph Ellersgaard and Stefan Andrade
Maintainer: Anton Grau Larsen <alar@soc.ku.dk>

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Package simPop updated to version 0.2.12 with previous version 0.2.9 dated 2015-01-26

Title: Simulation of Synthetic Populations for Survey Data Considering Auxiliary Information
Description: Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ<matthias.templ@gmail.com>

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New package PanelCount with initial version 1.0.1
Package: PanelCount
Type: Package
Title: Random Effects and Sample Selection Models for Panel Counting Data
Version: 1.0.1
Date: 2015-08-30
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Description: A High Performance Package Implementing Random Effects and Sample Selection Models for Panel Counting Data.
License: GPL (>= 3)
LazyData: TRUE
Depends: R (>= 3.0.0)
Imports: Rcpp, statmod, stats, utils
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-08-30 19:01:28 UTC; Peng
Repository: CRAN
Date/Publication: 2015-08-31 14:48:46

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Package ms.sev updated to version 1.0.1 with previous version 1.0 dated 2015-08-26

Title: Package for Calculation of ARMSS, Local MSSS and Global MSSS
Description: Calculates ARMSS, age related multiple sclerosis severity score, and both local and global msss.
Author: Helga Westerlind, Ali Manouchehrinia
Maintainer: Helga Westerlind <Helga.Westerlind@ki.se>

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Package gMCP updated to version 0.8-10 with previous version 0.8-9 dated 2015-08-10

Title: Graph Based Multiple Comparison Procedures
Description: Functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>

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Package erer updated to version 2.4 with previous version 2.3 dated 2014-11-27

Title: Empirical Research in Economics with R
Description: Functions, datasets, and sample codes related to the book of 'Empirical Research in Economics: Growing up with R' by Dr. Changyou Sun are included. Marginal effects for binary or ordered choice models can be calculated. Static and dynamic Almost Ideal Demand System (AIDS) models can be estimated. A typical event analysis in finance can be conducted with several functions included.
Author: Changyou Sun <cs258@msstate.edu>
Maintainer: Changyou Sun <cs258@msstate.edu>

Diff between erer versions 2.3 dated 2014-11-27 and 2.4 dated 2015-08-31

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More information about erer at CRAN
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Package dawai updated to version 1.2.1 with previous version 1.2 dated 2015-08-13

Title: Discriminant Analysis with Additional Information
Description: In applications it is usual that some additional information is available. This package dawai (an acronym for Discriminant Analysis With Additional Information) performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means. It also computes several estimations of the true error rate.
Author: David Conde, Miguel A. Fernandez, Bonifacio Salvador
Maintainer: David Conde <dconde@eio.uva.es>

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Package clusterCrit updated to version 1.2.6 with previous version 1.2.5 dated 2015-06-04

Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>

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Permanent link

New package abodOutlier with initial version 0.1
Package: abodOutlier
Title: Angle-Based Outlier Detection
Version: 0.1
Author: Jose Jimenez <jose@jimenezluna.com>
Maintainer: Jose Jimenez <jose@jimenezluna.com>
Description: Performs angle-based outlier detection on a given dataframe. Three methods are available, a full but slow implementation using all the data that has cubic complexity, a fully randomized one which is way more efficient and another using k-nearest neighbours. These algorithms are specially well suited for high dimensional data outlier detection.
Depends: cluster, R (>= 3.1.2)
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2015-08-30 21:39:13 UTC; hawk31
Repository: CRAN
Date/Publication: 2015-08-31 14:31:42

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Sun, 30 Aug 2015

Package rmarkdown updated to version 0.8 with previous version 0.7 dated 2015-06-13

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between rmarkdown versions 0.7 dated 2015-06-13 and 0.8 dated 2015-08-30

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Package npmv updated to version 2.3.0 with previous version 2.2 dated 2015-02-25

Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis <arelli4@uky.edu>

Diff between npmv versions 2.2 dated 2015-02-25 and 2.3.0 dated 2015-08-30

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Package RcppGSL updated to version 0.3.0 with previous version 0.2.5 dated 2015-07-07

Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines such as special functions, permutations, combinations, fast fourier transforms, eigensystems, random numbers, quadrature, random distributions, quasi-random sequences, Monte Carlo integration, N-tuples, differential equations, simulated annealing, numerical differentiation, interpolation, series acceleration, Chebyshev approximations, root-finding, discrete Hankel transforms physical constants, basis splines and wavelets. There are over 1000 functions in total with an extensive test suite. The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses 'Rcpp' to connect to another third-party library. The 'autoconf' script, 'inline' plugin and example package can all be used as a stanza to write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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New package humaniformat with initial version 0.5.0
Package: humaniformat
Title: A Parser for Human Names
Version: 0.5.0
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Description: Human names are complicated and nonstandard things. Humaniformat, which is based on Anthony Ettinger's 'humanparser' project (https://github.com/chovy/humanparser) provides functions for parsing human names, making a best-guess attempt to distinguish sub-components such as prefixes, suffixes, middle names and salutations.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/ironholds/humaniformat/
BugReports: https://github.com/ironholds/humaniformat/issues
Suggests: testthat, knitr
LinkingTo: Rcpp
Imports: Rcpp, methods
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-08-30 13:58:09 UTC; ironholds
Repository: CRAN
Date/Publication: 2015-08-30 16:15:58

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Package WufooR updated to version 0.5.7 with previous version 0.5.5 dated 2015-07-17

Title: R Wrapper for the 'Wufoo.com' - The Form Building Service
Description: Allows form managers to download entries from their respondents using Wufoo JSON API. Additionally, the Wufoo reports - when public - can be also acquired programmatically. Note that building new forms within this package is not supported.
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>

Diff between WufooR versions 0.5.5 dated 2015-07-17 and 0.5.7 dated 2015-08-30

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Package spatial updated to version 7.3-11 with previous version 7.3-10 dated 2015-06-29

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between spatial versions 7.3-10 dated 2015-06-29 and 7.3-11 dated 2015-08-30

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Package robustlmm updated to version 1.7-6 with previous version 1.7-4 dated 2015-07-14

Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly. Robustness is achieved by modification of the scoring equations combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>

Diff between robustlmm versions 1.7-4 dated 2015-07-14 and 1.7-6 dated 2015-08-30

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Package psych updated to version 1.5.8 with previous version 1.5.6 dated 2015-07-08

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox for personality, psychometrics 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 multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating 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 psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>

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Package nnet updated to version 7.3-11 with previous version 7.3-10 dated 2015-06-29

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package dotwhisker updated to version 0.2.0.0 with previous version 0.1.0.1 dated 2015-07-28

Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

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Package class updated to version 7.3-14 with previous version 7.3-13 dated 2015-06-29

Title: Functions for Classification
Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Sat, 29 Aug 2015

Package TAM updated to version 1.13-0 with previous version 1.12-0 dated 2015-08-27

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

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Package PRIMsrc updated to version 0.5.8 with previous version 0.5.7 dated 2015-07-28

Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>

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Package MFAg updated to version 1.1 with previous version 1.0 dated 2015-08-21

Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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New package xseq with initial version 0.2.0
Package: xseq
Title: Assessing Functional Impact on Gene Expression of Mutations in Cancer
Version: 0.2.0
Date: 2015-08-25
Author: Jiarui Ding, Sohrab Shah
Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>
Depends: R (>= 3.1.0)
Imports: e1071 (>= 1.6-4), gptk (>= 1.08), impute (>= 1.42.0), preprocessCore (>= 1.30.0), RColorBrewer (>= 1.1-2), sfsmisc (>= 1.0-27)
Suggests: knitr
Description: A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients; and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.
License: GPL (>= 2)
LazyLoad: ture
Packaged: 2015-08-29 19:53:11 UTC; jding
VignetteBuilder: knitr
LazyData: TRUE
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-08-29 23:04:29

More information about xseq at CRAN
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Package smacpod updated to version 1.2.3 with previous version 1.1.1 dated 2014-11-18

Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data. The methods available closely follow those in chapter 6 of Applied Spatial Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>

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Package reutils updated to version 0.2.1 with previous version 0.1.2 dated 2014-02-26

Title: Talk to the NCBI EUtils
Description: An interface to NCBI databases such as PubMed, GenBank, or GEO powered by the Entrez Programming Utilities (EUtils). The nine EUtils provide programmatic access to the NCBI Entrez query and database system for searching and retrieving biological data.
Author: Gerhard Schöfl <gerhard.schofl@gmail.com>
Maintainer: Gerhard Schöfl <gerhard.schofl@gmail.com>

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Package FlexParamCurve updated to version 1.5-3 with previous version 1.5-2 dated 2015-04-01

Title: Tools to Fit Flexible Parametric Curves
Description: Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
Author: Stephen Oswald [aut, cre]
Maintainer: Stephen Oswald <steve.oswald@psu.edu>

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 man/FlexParamCurve-package.Rd |    8 ++
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New package docxtractr with initial version 0.1.0.9000
Package: docxtractr
Title: Extract Data Tables from Microsoft Word Documents
Version: 0.1.0.9000
Authors@R: c(person("Bob", "Rudis", email = "bob@rudis.net", role = c("aut", "cre")))
Maintainer: Bob Rudis <bob@rudis.net>
Description: Microsoft Word docx files provide an XML structure that is fairly straightforward to navigate, especially when it applies to Word tables. The docxtractr package provides tools to determine table count/structure and extract/clean tables from Microsoft Word docx documents.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
Suggests: testthat
Imports: tools, xml2, dplyr, utils
NeedsCompilation: no
Packaged: 2015-08-28 23:08:34 UTC; bob
Author: Bob Rudis [aut, cre]
Repository: CRAN
Date/Publication: 2015-08-29 13:15:01

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New package dml with initial version 1.1.0
Package: dml
Version: 1.1.0
Date: 2015-08-26
Title: Distance Metric Learning in R
Description: The state-of-the-art algorithms for distance metric learning, including global and local methods such as Relevant Component Analysis, Discriminative Component Analysis, Local Fisher Discriminant Analysis, etc. These distance metric learning methods are widely applied in feature extraction, dimensionality reduction, clustering, classification, information retrieval, and computer vision problems.
Depends: MASS
Imports: lfda
Suggests: testthat
Author: Yuan Tang <terrytangyuan@gmail.com>, Gao Tao <joegaotao@gmail.com>, Xiao Nan <road2stat@gmail.com>
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
License: MIT + file LICENSE
URL: https://github.com/terrytangyuan/dml
BugReports: https://github.com/terrytangyuan/dml/issues
NeedsCompilation: no
Packaged: 2015-08-28 15:32:47 UTC; Yuan
Repository: CRAN
Date/Publication: 2015-08-29 13:14:59

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Package ConSpline updated to version 1.1 with previous version 1.0 dated 2015-03-30

Title: Partial Linear Least-Squares Regression using Constrained Splines
Description: Given response y, continuous predictor x, and covariate matrix, the relationship between E(y) and x is estimated with a shape constrained regression spline. Function outputs fits and various types of inference.
Author: Mary C Meyer
Maintainer: Mary C Meyer <meyer@stat.colostate.edu>

Diff between ConSpline versions 1.0 dated 2015-03-30 and 1.1 dated 2015-08-29

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Package CDM updated to version 4.5-0 with previous version 4.4-1 dated 2015-07-01

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between CDM versions 4.4-1 dated 2015-07-01 and 4.5-0 dated 2015-08-29

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 31 files changed, 218 insertions(+), 131 deletions(-)

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Package beeswarm updated to version 0.2.1 with previous version 0.2.0 dated 2015-05-04

Title: The Bee Swarm Plot, an Alternative to Stripchart
Description: The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.
Author: Aron Eklund
Maintainer: Aron Eklund <eklund@cbs.dtu.dk>

Diff between beeswarm versions 0.2.0 dated 2015-05-04 and 0.2.1 dated 2015-08-29

 DESCRIPTION |   12 ++++++------
 MD5         |    7 ++++---
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New package rwunderground with initial version 0.1.0
Package: rwunderground
Type: Package
Title: R Interface to Weather Underground API
Version: 0.1.0
Date: 2015-08-24
Author: Alex Shum <alex@ALShum.com>
Maintainer: Alex Shum <alex@ALShum.com>
Description: Tools for getting historical weather information and forecasts from wunderground.com. Historical weather and forecast data includes, but is not limited to, temperature, humidity, windchill, wind speed, dew point, heat index. Additionally, the weather underground weather API also includes information on sunrise/sunset, tidal conditions, satellite/webcam imagery, weather alerts, hurricane alerts and historical record high/low temperatures.
URL: https://github.com/ALShum/rwunderground, http://www.wunderground.com/weather/api
BugReports: https://github.com/alshum/rwunderground/issues
License: GPL (>= 2)
Imports: httr, dplyr, countrycode
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-08-28 17:00:55 UTC; MKULTRA
Repository: CRAN
Date/Publication: 2015-08-29 09:40:05

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Package restorepoint updated to version 0.1.7 with previous version 0.1.5 dated 2014-02-20

Title: Debugging with Restore Points
Description: Debugging with restore points instead of break points. A restore point stores all local variables when called inside a function. The stored values can later be retrieved and evaluated in a modified R console that replicates the function's environment. To debug step by step, one can simply copy & paste the function body from the R script. Particularly convenient in combination with RStudio. See the github page for a tutorial.
Author: Sebastian Kranz
Maintainer: Sebastian Kranz <sebastian.kranz@uni-ulm.de>

Diff between restorepoint versions 0.1.5 dated 2014-02-20 and 0.1.7 dated 2015-08-29

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 restorepoint-0.1.7/restorepoint/man/can.parse.multi.line.Rd           |   12 
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 26 files changed, 549 insertions(+), 320 deletions(-)

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New package pnea with initial version 1.0.1
Package: pnea
Type: Package
Title: Parametric Network Enrichment Analysis
Version: 1.0.1
Date: 2015-08-28
Depends: R (>= 3.2.0)
Author: Mirko Signorelli
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Description: Collection of functions for Parametric Network Enrichment Analysis.
Suggests: igraph
License: GPL-3
NeedsCompilation: no
Packaged: 2015-08-28 15:04:40 UTC; Mirko
Repository: CRAN
Date/Publication: 2015-08-29 09:45:48

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Package mixOmics updated to version 5.1.2 with previous version 5.1.1 dated 2015-07-30

Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and variants to analyse highly dimensional data sets: regularized Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS') to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>

Diff between mixOmics versions 5.1.1 dated 2015-07-30 and 5.1.2 dated 2015-08-29

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Package lsmeans updated to version 2.20 with previous version 2.19 dated 2015-07-26

Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre], Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

Diff between lsmeans versions 2.19 dated 2015-07-26 and 2.20 dated 2015-08-29

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Fri, 28 Aug 2015

Package trimr updated to version 1.0.1 with previous version 1.0.0 dated 2015-08-02

Title: An Implementation of Common Response Time Trimming Methods
Description: Provides various commonly-used response time trimming methods, including the recursive / moving-criterion methods reported by Van Selst and Jolicoeur (1994). By passing trimming functions raw data files, the package will return trimmed data ready for inferential testing.
Author: James Grange [aut, cre]
Maintainer: James Grange <grange.jim@gmail.com>

Diff between trimr versions 1.0.0 dated 2015-08-02 and 1.0.1 dated 2015-08-28

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New package wec with initial version 0.1
Package: wec
Type: Package
Title: Weighted Effect Coding
Version: 0.1
Date: 2015-09-05
Author: Rense Nieuwenhuis, Manfred te Grotenhuis, Ben Pelzer, Alexanter Schmidt, Ruben Konig, Rob Eisinga
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Description: Provides functions to create factor variables with contrasts based on weighted effect coding. In weighted effect coding the estimates from a first order regression model show the deviations per group from the sample mean. This is especially useful when a researcher has no directional hypotheses and uses a sample from a population in which the number of observation per group is different The package also provides functionality for interactions between two factor variables based on weighted effect coding. Please note that this is a beta version: while functional, it does not follow all R conventions.
License: GPL-3
NeedsCompilation: no
Packaged: 2015-08-28 05:40:08 UTC; rensenieuwenhuis
Repository: CRAN
Date/Publication: 2015-08-28 16:37:03

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New package OriGen with initial version 1.3
Package: OriGen
Type: Package
Title: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Version: 1.3
Author: John Michael O Ranola, John Novembre, and Kenneth Lange
Depends: maps, ggplot2
Maintainer: John Michael O. Ranola <ranolaj@uw.edu>
Description: Used primarily for estimates of allele frequency surfaces from point estimates. It can also place individuals of unknown origin back onto the geographic map with great accuracy. Additionally, it can place admixed individuals by estimating contributing fractions at each location on a map. Lastly, it can rank SNPs by their ability to differentiate populations. See "Fast Spatial Ancestry via Flexible Allele Frequency Surfaces" (John Michael Ranola, John Novembre, Kenneth Lange) in Bioinformatics 2014 for more info.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: origen
Repository/R-Forge/Revision: 16
Repository/R-Forge/DateTimeStamp: 2015-08-27 22:57:54
Date/Publication: 2015-08-28 16:36:53
NeedsCompilation: yes
Packaged: 2015-08-27 23:05:10 UTC; rforge

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Package kin.cohort updated to version 0.7 with previous version 0.6 dated 2009-01-29

Title: Analysis of Kin-Cohort Studies
Description: Analysis of kin-cohort studies. kin.cohort provides estimates of age-specific cumulative risk of a disease for carriers and noncarriers of a mutation. The cohorts are retrospectively built from relatives of probands for whom the genotype is known. Currently the method of moments and marginal maximum likelihood are implemented. Confidence intervals are calculated from bootstrap samples. Most of the code is a translation from previous 'MATLAB' code by N. Chatterjee.
Author: Victor Moreno, Nilanjan Chatterjee, Bhramar Mukherjee
Maintainer: Victor Moreno <v.moreno@iconcologia.net>

Diff between kin.cohort versions 0.6 dated 2009-01-29 and 0.7 dated 2015-08-28

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Package geesmv updated to version 1.2 with previous version 1.1 dated 2015-05-29

Title: Modified Variance Estimators for Generalized Estimating Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>

Diff between geesmv versions 1.1 dated 2015-05-29 and 1.2 dated 2015-08-28

 DESCRIPTION    |   10 -
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 NAMESPACE      |    1 
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 5 files changed, 158 insertions(+), 157 deletions(-)

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Package erboost updated to version 1.3 with previous version 1.2 dated 2013-10-28

Title: Nonparametric Multiple Expectile Regression via ER-Boost
Description: Expectile regression is a nice tool for estimating the conditional expectiles of a response variable given a set of covariates. This package implements a regression tree based gradient boosting estimator for nonparametric multiple expectile regression.
Author: Yi Yang <yiyang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Yi Yang <yiyang@umn.edu>

Diff between erboost versions 1.2 dated 2013-10-28 and 1.3 dated 2015-08-28

 ChangeLog                 |    3 +++
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 MD5                       |   18 +++++++++---------
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 10 files changed, 67 insertions(+), 51 deletions(-)

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Package CMplot updated to version 3.0.1 with previous version 2.0.1 dated 2015-06-16

Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>

Diff between CMplot versions 2.0.1 dated 2015-06-16 and 3.0.1 dated 2015-08-28

 DESCRIPTION           |   10 +-
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 5 files changed, 206 insertions(+), 83 deletions(-)

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Thu, 27 Aug 2015

New package lookupTable with initial version 0.1
Package: lookupTable
Type: Package
Title: Look-Up Tables using S4
Version: 0.1
Date: 2015-08-17
Authors@R: c(person('Enzo', 'Jia', email = 'enzo.jia@gmail.com', role = c('aut', 'cre')), person('Marc', 'Maier', email = 'mmaier@massmutual.com', role = 'aut'))
Maintainer: Enzo Jia <enzo.jia@gmail.com>
Description: Fits look-up tables by filling entries with the mean or median values of observations fall in partitions of the feature space. Partitions can be determined by user of the package using input argument feature.boundaries, and dimensions of the feature space can be any combination of continuous and categorical features provided by the data set. A Predict function directly fetches corresponding entry value, and a default value is defined as the mean or median of all available observations. The table and other components are represented using the S4 class lookupTable.
License: MIT + file LICENSE
LazyData: TRUE
Imports: dplyr, methods
Depends: data.table
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-08-27 13:26:20 UTC; mm87727
Author: Enzo Jia [aut, cre], Marc Maier [aut]
Repository: CRAN
Date/Publication: 2015-08-28 01:21:23

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New package kerndwd with initial version 1.0.1
Package: kerndwd
Type: Package
Title: Distance Weighted Discrimination (DWD) and Kernel Methods
Version: 1.0.1
Date: 2015-08-27
Author: Boxiang Wang <boxiang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Boxiang Wang <boxiang@umn.edu>
Description: A very efficient implementation that solves the generalized DWD under any kernel regularization.
Depends: methods
Imports: graphics, grDevices, stats, utils
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
Packaged: 2015-08-27 16:21:16 UTC; Boxiang
Date/Publication: 2015-08-28 01:18:19

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New package GsymPoint with initial version 1.0
Package: GsymPoint
Type: Package
Title: Estimation of the Generalized Symmetry Point, an Optimal Cutpoint in Continuous Diagnostic Tests
Version: 1.0
Date: 2015-08-27
Depends: truncnorm, Rsolnp
Author: Mnica Lpez-Ratn, Carmen Cadarso-Surez, Elisa M. Molanes-Lpez, Emilio Letn
Maintainer: Mnica Lpez-Ratn
Description: Estimation of the cutpoint defined by the Generalized Symmetry point in a binary classification setting based on a continuous diagnostic test or marker. Two methods have been implemented to construct confidence intervals for this optimal cutpoint, one based on the Generalized Pivotal Quantity and the other based on Empirical Likelihood. Numerical and graphical outputs for these two methods are easily obtained.
License: GPL
Encoding: latin1
Packaged: 2015-08-27 20:47:04 UTC; Mari
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-28 01:20:23

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New package detector with initial version 0.1.0
Package: detector
Title: Detect Data Containing Personally Identifiable Information
Version: 0.1.0
Description: Allows users to quickly and easily detect data containing Personally Identifiable Information (PII) through convenience functions.
Authors@R: person("Paul", "Hendricks", , "paul.hendricks.2013@owu.edu", c("aut", "cre"))
URL: https://github.com/paulhendricks/detector
BugReports: https://github.com/paulhendricks/detector/issues
Depends: R (>= 3.1.2)
License: MIT + file LICENSE
LazyData: true
Imports: stringr
Suggests: testthat, generator
NeedsCompilation: no
Packaged: 2015-08-27 19:58:34 UTC; phendricks
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Repository: CRAN
Date/Publication: 2015-08-28 01:13:37

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New package apaTables with initial version 1.0.3
Package: apaTables
Title: Create American Psychological Association (APA) Style Tables
Version: 1.0.3
Authors@R: person("David", "Stanley", , "dstanley@uoguelph.ca", role = c("aut", "cre"))
Description: A common task faced by researchers is the creation of APA style (i.e., American Psychological Association style) tables from statistical output. In R a large number of function calls are often needed to obtain all of the desired information for a single APA style table. As well, the process of manually creating APA style tables in a word processor is prone to transcription errors. This package creates Word files (.doc files) containing APA style tables for several types of analyses. Using this package minimizes transcription errors and reduces the number commands needed by the user.
Depends: R (>= 3.1.2)
Date: 2015-08-27
License: Unlimited
LazyData: true
Imports: rockchalk, stats, utils, methods, MBESS, car
NeedsCompilation: no
Packaged: 2015-08-27 14:57:56 UTC; stanley
Author: David Stanley [aut, cre]
Maintainer: David Stanley <dstanley@uoguelph.ca>
Repository: CRAN
Date/Publication: 2015-08-28 01:13:36

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Package ALTopt updated to version 0.1.1 with previous version 0.1.0 dated 2015-01-17

Title: Optimal Experimental Designs for Accelerated Life Testing
Description: Creates the optimal (D, U and I) designs for the accelerated life testing with right censoring or interval censoring. It uses generalized linear model (GLM) approach to derive the asymptotic variance-covariance matrix of regression coefficients. The failure time distribution is assumed to follow Weibull distribution with a known shape parameter and log-linear link functions are used to model the relationship between failure time parameters and stress variables. The acceleration model may have multiple stress factors, although most ALTs involve only two or less stress factors. ALTopt package also provides several plotting functions including contour plot, Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space (VDUS) plot.
Author: Kangwon Seo [aut, cre], Rong Pan [aut]
Maintainer: Kangwon Seo <kseo7@asu.edu>

Diff between ALTopt versions 0.1.0 dated 2015-01-17 and 0.1.1 dated 2015-08-27

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New package umx with initial version 0.50
Package: umx
Version: 0.50
Date: 2015-08-27
Title: Helper Functions for Structural Equation Modelling in OpenMx
Authors@R: c(person("Timothy C", "Bates", role = c("aut", "cre"), email = "timothy.c.bates@gmail.com"))
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
License: GPL-3
URL: http://github.com/tbates/umx
Description: Helper functions for making, running, and reporting SEM models in OpenMx. If you are just starting, try typing ?umx.
Depends: R (>= 3.0.3), OpenMx (>= 2.2.0)
Imports: formula.tools, utils, MASS, Matrix, methods, mvtnorm, numDeriv, polycor, R2HTML, RCurl
Suggests: knitr
BugReports: http://github.com/tbates/umx/issues
LazyData: true
NeedsCompilation: no
Packaged: 2015-08-27 14:06:02 UTC; tim
Author: Timothy C Bates [aut, cre]
Repository: CRAN
Date/Publication: 2015-08-28 01:11:25

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Package tmvtnorm updated to version 1.4-10 with previous version 1.4-9 dated 2014-03-03

Title: Truncated Multivariate Normal and Student t Distribution
Description: Random number generation for the truncated multivariate normal and Student t distribution. Computes probabilities, quantiles and densities, including one-dimensional and bivariate marginal densities. Computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.
Author: Stefan Wilhelm <wilhelm@financial.com> with contributions from Manjunath B G <bgmanjunath@gmail.com>
Maintainer: Stefan Wilhelm <wilhelm@financial.com>

Diff between tmvtnorm versions 1.4-9 dated 2014-03-03 and 1.4-10 dated 2015-08-27

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 NAMESPACE                 |    1 +
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Package mpt updated to version 0.5-2 with previous version 0.5-1 dated 2015-02-03

Title: Multinomial Processing Tree Models
Description: Fitting and testing multinomial processing tree (MPT) models, a class of statistical models for categorical data. The parameters are the link probabilities of a tree-like graph and represent the latent cognitive processing steps executed to arrive at observable response categories (Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer & Batchelder, 1988).
Author: Florian Wickelmaier [aut, cre], Achim Zeileis [aut]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>

Diff between mpt versions 0.5-1 dated 2015-02-03 and 0.5-2 dated 2015-08-27

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 6 files changed, 54 insertions(+), 35 deletions(-)

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New package KERE with initial version 1.0.0
Package: KERE
Title: Expectile Regression in Reproducing Kernel Hilbert Space
Version: 1.0.0
Date: 2015-8-26
Author: Yi Yang, Teng Zhang, Hui Zou
Maintainer: Yi Yang <yiyang@umn.edu>
Depends: methods
Description: An efficient algorithm inspired by majorization-minimization principle for solving the entire solution path of a flexible nonparametric expectile regression estimator constructed in a reproducing kernel Hilbert space.
License: GPL-2
Packaged: 2015-08-27 13:38:41 UTC; emeryyi
Repository: CRAN
Date/Publication: 2015-08-28 00:35:09
NeedsCompilation: yes

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New package hdnom with initial version 1.2
Package: hdnom
Type: Package
Title: Nomograms for High-Dimensional Cox Models
Version: 1.2
Date: 2015-08-27
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
License: GPL
LazyData: TRUE
VignetteBuilder: knitr
URL: http://nomogr.am
BugReports: https://github.com/road2stat/hdnom/issues
Depends: R (>= 3.0.2)
Imports: survival, glmnet, rms, foreach, survAUC
Suggests: knitr, doParallel, Hmisc, mice
NeedsCompilation: no
Packaged: 2015-08-27 14:07:40 UTC; jimmy
Repository: CRAN
Date/Publication: 2015-08-28 01:11:22

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Package extRemes updated to version 2.0-6 with previous version 2.0-5 dated 2015-01-21

Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>

Diff between extRemes versions 2.0-5 dated 2015-01-21 and 2.0-6 dated 2015-08-27

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Package cacIRT updated to version 1.4 with previous version 1.3 dated 2014-01-28

Title: Classification Accuracy and Consistency under Item Response Theory
Description: Computes classification accuracy and consistency indices under Item Response Theory. Implements the total score IRT-based methods in Lee, Hanson & Brennen (2002) and Lee (2010), the IRT-based methods in Rudner (2001, 2005), and the total score nonparametric methods in Lathrop & Cheng (2014). For dichotomous and polytomous tests.
Author: Quinn N. Lathrop
Maintainer: Quinn N. Lathrop <quinn.lathrop@gmail.com>

Diff between cacIRT versions 1.3 dated 2014-01-28 and 1.4 dated 2015-08-27

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Package Anthropometry updated to version 1.5 with previous version 1.3 dated 2015-08-26

Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

Diff between Anthropometry versions 1.3 dated 2015-08-26 and 1.5 dated 2015-08-27

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Package walkr updated to version 0.3.3 with previous version 0.3-2 dated 2015-08-13

Title: Random Walks in the Intersection of Hyperplanes and the N-Simplex
Description: Consider the intersection of two spaces: the complete solution space to Ax = b and the N-simplex. The intersection of these two spaces is a non-negative convex polytope. The package walkr samples from this intersection using two Monte-Carlo Markov Chain (MCMC) methods: hit-and-run and Dikin walk. walkr also provide tools to examine sample quality.
Author: as.person(c( "Andy Yao <andy.yao17@gmail.com> [aut]", "David Kane <dave.kane@gmail.com> [aut]" ))
Maintainer: Andy Yao <andy.yao17@gmail.com>

Diff between walkr versions 0.3-2 dated 2015-08-13 and 0.3.3 dated 2015-08-27

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Package TAM updated to version 1.12-0 with previous version 1.11-0 dated 2015-08-11

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between TAM versions 1.11-0 dated 2015-08-11 and 1.12-0 dated 2015-08-27

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 6 files changed, 47 insertions(+), 20 deletions(-)

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New package SimReg with initial version 1.1
Package: SimReg
Type: Package
Title: Similarity Regression Functions
Version: 1.1
Date: 2015-08-26
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: Functions for performing Bayesian `similarity regression', adapted to regression of binary genotype against HPO encoded phenotype. The purpose is to weigh the evidence for an association between phenotype and genotype. This is done by estimating a Bayes factor comparing a `no association' model with one in which log odds of presenting a particular binary genotype is linked to the semantic similarity between the corresponding phenotype and an estimated characteristic phenotype.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.1), dplyr, parallel, ggplot2, plotrix, gridExtra, reshape2
LinkingTo: Rcpp
Depends: R (>= 3.0.0), hpoPlot
NeedsCompilation: yes
Packaged: 2015-08-27 09:19:17 UTC; dg333
Repository: CRAN
Date/Publication: 2015-08-27 14:14:04

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Package sgPLS updated to version 1.3 with previous version 1.2 dated 2015-04-30

Title: Sparse Group Partial Least Square Methods
Description: The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.
Author: Benoit Liquet and Pierre Lafaye de Micheaux
Maintainer: Benoit Liquet <b.liquet@uq.edu.au>

Diff between sgPLS versions 1.2 dated 2015-04-30 and 1.3 dated 2015-08-27

 DESCRIPTION        |    8 ++++----
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 NAMESPACE          |    2 ++
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New package edgar with initial version 1.0.1
Package: edgar
Type: Package
Title: Platform for EDGAR Filling Management
Version: 1.0.1
Date: 2015-08-24
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Depends: R (>= 3.1), shiny, shinydashboard, rChoiceDialogs
Imports: R.utils,tcltk,tm,XML,wordcloud,RColorBrewer
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR Master Index and EDGAR Fillings from SEC.org site and do sentiment analysis of 10-K statements.
License: GPL-2
Packaged: 2015-08-27 10:23:06 UTC; Gunratan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-27 14:14:11

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Package systemfit updated to version 1.1-18 with previous version 1.1-16 dated 2015-06-09

Title: Estimating Systems of Simultaneous Equations
Description: Fitting simultaneous systems of linear and nonlinear equations using Ordinary Least Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS).
Author: Arne Henningsen and Jeff D. Hamann
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between systemfit versions 1.1-16 dated 2015-06-09 and 1.1-18 dated 2015-08-27

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New package OptiQuantR with initial version 0.0.1
Package: OptiQuantR
Type: Package
Title: Simplifies and Automates Analyzing and Reporting OptiQuant's log Data
Version: 0.0.1
Date: 2015-08-24
Authors@R: person("Joao", "Pinelo Silva", email = "j.pinelo@mac.com", role = c("aut", "cre"))
Description: Greatly simplifies the process to read, analyze and report log data collated by OptiQuant (optiquant.opti55.com) in R. It automates efficient import of databases while preparing them for analysis and for semi-automated reporting.
Depends: R (>= 3.2.2)
Imports: data.table (>= 1.9.4), lubridate (>= 1.3.3)
License: GPL-3
LazyData: TRUE
Suggests: testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2015-08-27 07:39:59 UTC; jpinelo
Author: Joao Pinelo Silva [aut, cre]
Maintainer: Joao Pinelo Silva <j.pinelo@mac.com>
Repository: CRAN
Date/Publication: 2015-08-27 10:30:56

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Package multic updated to version 0.4.3 with previous version 0.4.2 dated 2015-08-21

Title: Quantitative Linkage Analysis Tools using the Variance Components Approach
Description: Calculate the polygenic and major gene models for quantitative trait linkage analysis using variance components approach. The 0.2.2 release includes bug fixes that allow 'multic' to run properly on 64-bit systems. The 0.3.0 release includes a fully implemented sw2mloci() function. As of 0.3.8, Splus version is no longer supported. Additional documentation and examples can be found in the inst directory.
Author: Eric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Maintainer: Pat Votruba <votruba.patrick@mayo.edu>

Diff between multic versions 0.4.2 dated 2015-08-21 and 0.4.3 dated 2015-08-27

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 4 files changed, 69 insertions(+), 37 deletions(-)

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Package intervals updated to version 0.15.1 with previous version 0.15.0 dated 2014-09-19

Title: Tools for Working with Points and Intervals
Description: Tools for working with and comparing sets of points and intervals.
Author: Richard Bourgon <bourgon.richard@gene.com>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between intervals versions 0.15.0 dated 2014-09-19 and 0.15.1 dated 2015-08-27

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Package InformationValue updated to version 1.1.1 with previous version 1.1.0 dated 2015-08-04

Title: Performance Analysis and Companion Functions for Accuracy Improvement for Binary Classification Problems
Description: Provides companion function for analysing the performance of classification models. Also, provides function to optimise probability cut-off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, etc to aid accuracy improvement in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>

Diff between InformationValue versions 1.1.0 dated 2015-08-04 and 1.1.1 dated 2015-08-27

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New package cate with initial version 1.0.1
Package: cate
Type: Package
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation
Version: 1.0.1
Date: 2015-08-22
Authors@R: c(person("Jingshu", "Wang", email = "jingshuw@stanford.edu", role = c("aut")), person("Qingyuan", "Zhao", email = "qyzhao@stanford.edu", role = c("aut", "cre")))
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Imports: MASS, esaBcv, ruv, sva, corpcor, leapp
License: GPL-2
LazyData: TRUE
Packaged: 2015-08-26 03:29:53 UTC; qyzhao
Author: Jingshu Wang [aut], Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-27 09:08:54

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Package support.CEs updated to version 0.4-1 with previous version 0.3-3 dated 2015-04-27

Title: Basic Functions for Supporting an Implementation of Choice Experiments
Description: Provides seven basic functions that support an implementation of choice experiments.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

Diff between support.CEs versions 0.3-3 dated 2015-04-27 and 0.4-1 dated 2015-08-27

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Package plfMA updated to version 1.0.1 with previous version 1.0 dated 2015-08-19

Title: A GUI to View, Design and Export Various Graphs of Data
Description: Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>

Diff between plfMA versions 1.0 dated 2015-08-19 and 1.0.1 dated 2015-08-27

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New package nhanesA with initial version 0.4
Package: nhanesA
Version: 0.4
Date: 2015-08-26
Title: NHANES Data Retrieval
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Depends: R (>= 3.0.0)
Imports: stringr, Hmisc
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
License: GPL (>= 2)
LazyData: TRUE
URL: https://github.com/cjendres1/nhanes
Packaged: 2015-08-26 22:59:01 UTC; Endres
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-27 08:31:57

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Package mmod updated to version 1.3.1 with previous version 1.3.0 dated 2015-07-11

Title: Modern Measures of Population Differentiation
Description: Provides functions for measuring population divergence from genotypic data.
Author: David Winter [aut, cre], Peter Green [ctb], Zhian Kamvar [ctb], Thierry Gosselin [ctb]
Maintainer: David Winter <david.winter@gmail.com>

Diff between mmod versions 1.3.0 dated 2015-07-11 and 1.3.1 dated 2015-08-27

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Package lasvmR updated to version 0.1.2 with previous version 0.1.1 dated 2015-08-26

Title: A Simple Wrapper for the LASVM Solver
Description: This is a simple wrapper for the LASVM Solver (see http://leon.bottou.org/projects/lasvm). LASVM is basically an online variant of the SMO solver.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>

Diff between lasvmR versions 0.1.1 dated 2015-08-26 and 0.1.2 dated 2015-08-27

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Package iaQCA updated to version 0.8.7.0 with previous version 0.8.0.0 dated 2015-08-06

Title: The Irvine Robustness Assessment for Qualitative Comparative Analysis
Description: Test the robustness of a user's QCA solutions to randomness, using iraQCA. iaQCA is packaged with the irrQCA function, which provides recommendations for improving QCA solutions to reach typical significance levels.
Author: C. Ben Gibson [aut, cre], Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>

Diff between iaQCA versions 0.8.0.0 dated 2015-08-06 and 0.8.7.0 dated 2015-08-27

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Package cgdsr updated to version 1.2.5 with previous version 1.2.4 dated 2015-08-25

Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
Description: Provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>

Diff between cgdsr versions 1.2.4 dated 2015-08-25 and 1.2.5 dated 2015-08-27

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New package CensMixReg with initial version 0.5
Package: CensMixReg
Type: Package
Title: Modeling Censored Data Using Mixture Regression
Version: 0.5
Date: 2015-08-26
Author: Luis Benites Sanchez, Victor Hugo Lachos
Maintainer: Luis Benites Sanchez <lbenitesanchez@gmail.com>
Imports: mixsmsn
Description: Fit censored linear mixture regression model of Normal or Student-t distribution.
License: GPL (>= 2)
LazyData: TRUE
Packaged: 2015-08-26 23:28:54 UTC; luis
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-27 08:56:09

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New package artfima with initial version 1.0
Package: artfima
Type: Package
Title: Fit ARTFIMA Model
Version: 1.0
Date: 2015-08-25
Author: A. I. McLeod, Farzad Sabzikar, Mark M. Meerschaert
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Description: Fit and simulate ARTFIMA. Theoretical autocovariance function and spectral density function for stationary ARTFIMA.
Depends: R (>= 2.1.0)
Imports: ltsa, gsl
LazyLoad: yes
LazyData: yes
Classification/ACM: G.3, G.4, I.5.1
Classification/MSC: 62M10, 91B84
License: GPL (>= 2)
URL: http://www.stats.uwo.ca/faculty/aim
NeedsCompilation: no
Packaged: 2015-08-27 04:54:54 UTC; IanMcLeod
Repository: CRAN
Date/Publication: 2015-08-27 08:35:42

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Wed, 26 Aug 2015

Package sjPlot updated to version 1.8.3 with previous version 1.8.2 dated 2015-07-01

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 1.8.2 dated 2015-07-01 and 1.8.3 dated 2015-08-26

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Package sjmisc updated to version 1.1 with previous version 1.0.3 dated 2015-06-20

Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/or who are new to R), supporting following common tasks: 1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc. 2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. 3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package sisVIVE updated to version 1.2 with previous version 1.1 dated 2015-05-05

Title: Some Invalid Some Valid Instrumental Variables Estimator
Description: Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome.
Author: Hyunseung Kang <hskang@stanford.edu>
Maintainer: Hyunseung Kang <hskang@stanford.edu>

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Package SDDE updated to version 1.0.1 with previous version 1.0.0 dated 2015-03-06

Title: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
Description: Compares the evolution of an original network X to an augmented network Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal paths and disconnected nodes.
Author: Etienne Lord, Margaux Le Cam, Eric Bapteste, Vladimir Makarenkov and Francois-Joseph Lapointe
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>

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Package Rfit updated to version 0.22.0 with previous version 0.21 dated 2014-11-07

Title: Rank Estimation for Linear Models
Description: R estimation and inference for linear models. Estimation is for general scores and a library of commonly used score functions is included.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke <kloke@biostat.wisc.edu>

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Package multiway updated to version 1.0-1 with previous version 1.0-0 dated 2015-04-15

Title: Component Models for Multi-Way Data
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints (orthogonality and non-negativity). Fit models include Individual Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>

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New package ldamatch with initial version 0.6.3
Package: ldamatch
Title: Multivariate Condition Matching by Backwards Elimination Using Linear Discriminant Analysis
Version: 0.6.3
Authors@R: c(person("Kyle", "Gorman", email = "kylebgorman@gmail.com", role = c("aut", "cre")), person("Geza", "Kiss", email = "kiss@ohsu.edu", role = c("ctb")))
Description: Performs group matching by backward elimination using linear discriminant analysis.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
Imports: RUnit, data.table, foreach, kSamples, MASS, entropy, iterators, iterpc
NeedsCompilation: no
Packaged: 2015-08-26 11:47:34 UTC; kgorman
Author: Kyle Gorman [aut, cre], Geza Kiss [ctb]
Maintainer: Kyle Gorman <kylebgorman@gmail.com>
Repository: CRAN
Date/Publication: 2015-08-27 01:04:08

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Package googleVis updated to version 0.5.10 with previous version 0.5.9 dated 2015-07-04

Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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New package generator with initial version 0.1.0
Package: generator
Title: Generate Data Containing Fake Personally Identifiable Information
Version: 0.1.0
Description: Allows users to quickly and easily generate fake data containing Personally Identifiable Information (PII) through convenience functions.
Authors@R: person("Paul", "Hendricks", , "paul.hendricks.2013@owu.edu", c("aut", "cre"))
URL: https://github.com/paulhendricks/generator
BugReports: https://github.com/paulhendricks/generator/issues
Depends: R (>= 3.1.2)
License: MIT + file LICENSE
LazyData: true
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-08-26 15:43:39 UTC; phendricks
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Repository: CRAN
Date/Publication: 2015-08-26 23:11:56

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