Tue, 10 Jan 2017

Package pracma updated to version 1.9.9 with previous version 1.9.5 dated 2016-09-06

Title: Practical Numerical Math Functions
Description: Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Author: Hans Werner Borchers [aut, cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

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Package NetWeaver updated to version 0.0.2 with previous version 0.0.1 dated 2016-12-22

Title: Graphic Presentation of Complex Genomic and Network Data Analysis
Description: Implements various simple function utilities and flexible pipelines to generate circular images for visualizing complex genomic and network data analysis features.
Author: Minghui Wang, Bin Zhang
Maintainer: Minghui Wang <m.h.wang@live.com>

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Package goric updated to version 0.0-95 with previous version 0.0-8 dated 2014-11-16

Title: Generalized Order-Restricted Information Criterion for Selecting Order-Restricted (Multivariate) Linear Models
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate regression models.
Author: Daniel Gerhard [aut, cre], Rebecca M. Kuiper [aut]
Maintainer: Daniel Gerhard <00gerhard@gmail.com>

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New package COMBAT with initial version 0.0.2
Package: COMBAT
Type: Package
Title: A Combined Association Test for Genes using Summary Statistics
Version: 0.0.2
Date: 2017-01-10
Author: Minghui Wang, Jianfei Huang, James B. Potash, Shizhong Han
Maintainer: Minghui Wang <m.h.wang@live.com>
Description: To compute gene-based genetic association statistics from P values at multiple SNPs and genotype data of ancestry matched reference samples. COMBined Association Test (COMBAT) incorporates strengths from multiple existing gene-based tests, including VEGAS, GATES and SimpleM, and achieves much improved performance than any individual test.
Depends: mvtnorm, corpcor, R (>= 3.2.0)
Suggests: parallel
License: GPL-2
NeedsCompilation: no
Packaged: 2017-01-10 21:16:05 UTC; Minghui
Repository: CRAN
Date/Publication: 2017-01-11 01:49:37

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Package BASS updated to version 0.2.0 with previous version 0.1.0 dated 2016-12-16

Title: Bayesian Adaptive Spline Surfaces
Description: Bayesian fitting and sensitivity analysis methods for adaptive spline surfaces. Built to handle continuous and categorical inputs as well as functional or scalar output. An extension of the methodology in Denison, Mallick and Smith (1998) <doi:10.1023/A:1008824606259>.
Author: Devin Francom [aut, cre], Bruno Sanso [ths], Agner Fog [ctb, cph]
Maintainer: Devin Francom <devinfrancom@gmail.com>

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Package xxIRT updated to version 2.0.0 with previous version 1.1.0 dated 2016-08-29

Title: Practical Item Response Theory and Computer-Based Testing in R
Description: An implementation of item response theory (IRT) and computer-based testing in R. It is designed for bridging the gap between theoretical advancements in psychometric research and their applications in practice. Currently, it consists of five modules: (1) common IRT functions, (2) estimation procedures, (3) automated test assembly framework, (4) computerized adaptive testing framework, (5) multistage testing framework. See detailed documentation at <https://github.com/xluo11/xxIRT/blob/master/README.md>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>

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Package textTinyR updated to version 1.0.1 with previous version 1.0.0 dated 2017-01-07

Title: Text Processing for Small or Big Data Files
Description: Processes big text data files in batches efficiently. For this purpose, it offers functions for splitting, parsing, tokenizing and creating a vocabulary. Moreover, it includes functions for building either a document-term matrix or a term-document matrix and extracting information from those (term-associations, most frequent terms). Lastly, it embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package splines2 updated to version 0.2.4 with previous version 0.2.3 dated 2016-12-10

Title: Regression Spline Functions and Classes Too
Description: A complementary package on splines providing functions constructing B-splines, integral of B-splines, monotone splines (M-splines) and its integral (I-splines), convex splines (C-splines), and their derivatives of given order. Piecewise constant basis is allowed for B-spline and M-spline basis.
Author: Wenjie Wang [aut, cre], Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

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Package RND updated to version 1.2 with previous version 1.1 dated 2014-03-22

Title: Risk Neutral Density Extraction Package
Description: Extract the implied risk neutral density from options using various methods.
Author: Kam Hamidieh <khamidieh@gmail.com>
Maintainer: Kam Hamidieh <khamidieh@gmail.com>

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Package NNS updated to version 0.2.5 with previous version 0.2.4 dated 2016-11-28

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. All routines based on ( Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995) ).
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>

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Package MALDIquant updated to version 1.16.1 with previous version 1.16 dated 2016-12-13

Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

Diff between MALDIquant versions 1.16 dated 2016-12-13 and 1.16.1 dated 2017-01-10

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Package RStoolbox updated to version 0.1.7 with previous version 0.1.6 dated 2016-11-07

Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as calculating spectral indices, principal component transformation, unsupervised and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut], Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>

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Permanent link

Package regclass updated to version 1.5 with previous version 1.4 dated 2016-08-06

Title: Tools for an Introductory Class in Regression and Modeling
Description: Contains basic tools for visualizing, interpreting, and building regression models. It has been designed for use with the book Introduction to Regression and Modeling with R by Adam Petrie, Cognella Publishers, ISBN: 978-1-63189-250-9 <https://titles.cognella.com/behavioral-and-social-sciences/general-social-sciences/introduction-to-regression-and-modeling-with-r-9781631892509.html>.
Author: Adam Petrie
Maintainer: Adam Petrie <apetrie@utk.edu>

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Permanent link

New package sparkwarc with initial version 0.1.0
Package: sparkwarc
Type: Package
Title: Load WARC Files into Apache Spark
Version: 0.1.0
Authors@R: c( person("Javier", "Luraschi", email = "javier@rstudio.com", role = c("aut", "cre")) )
Maintainer: Javier Luraschi <javier@rstudio.com>
Description: Load WARC (Web ARChive) files into Apache Spark using 'sparklyr'. This allows to read files from the Common Crawl project <http://commoncrawl.org/>.
License: Apache License 2.0
BugReports: https://github.com/javierluraschi/sparkwarc
Encoding: UTF-8
LazyData: true
Imports: sparklyr, DBI
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-10 17:33:15 UTC; javierluraschi
Author: Javier Luraschi [aut, cre]
Repository: CRAN
Date/Publication: 2017-01-10 19:03:56

More information about sparkwarc at CRAN
Permanent link

Package rgl updated to version 0.97.0 with previous version 0.96.0 dated 2016-08-25

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

Diff between rgl versions 0.96.0 dated 2016-08-25 and 0.97.0 dated 2017-01-10

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Permanent link

New package reprex with initial version 0.1.0
Package: reprex
Title: Prepare Reproducible Example Code for Sharing
Version: 0.1.0
Authors@R: c( person("Jennifer", "Bryan", , "jenny.f.bryan@gmail.com", role = c("aut", "cre")), person("David", "Robinson", , "admiral.david@gmail.com", role = "aut") )
Description: Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <http://stackoverflow.com> and <https://github.com>, or in email. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.
Depends: R (>= 3.0.2)
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/jennybc/reprex
BugReports: https://github.com/jennybc/reprex/issues
Imports: callr, clipr (>= 0.3.0), knitr, rmarkdown, tools, utils, whisker
Suggests: covr, devtools, formatR, fortunes, miniUI, rstudioapi, shiny, shinyjs, testthat
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2017-01-09 16:47:48 UTC; jenny
Author: Jennifer Bryan [aut, cre], David Robinson [aut]
Maintainer: Jennifer Bryan <jenny.f.bryan@gmail.com>
Repository: CRAN
Date/Publication: 2017-01-10 18:51:31

More information about reprex at CRAN
Permanent link

Package OpenMx updated to version 2.7.2 with previous version 2.6.9 dated 2016-07-28

Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others.
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut], Yang Wang [ctb], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph], Stefan Wilhelm [cph], Manjunath B G [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.6.9 dated 2016-07-28 and 2.7.2 dated 2017-01-10

 OpenMx-2.6.9/OpenMx/src/omxRAMExpectation.h                                                           |only
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 OpenMx-2.7.2/OpenMx/DESCRIPTION                                                                       |   26 
 OpenMx-2.7.2/OpenMx/MD5                                                                               | 1217 +++++-----
 OpenMx-2.7.2/OpenMx/NAMESPACE                                                                         |    2 
 OpenMx-2.7.2/OpenMx/NEWS                                                                              |  182 -
 OpenMx-2.7.2/OpenMx/R/0ClassUnion.R                                                                   |    2 
 OpenMx-2.7.2/OpenMx/R/DefinitionVars.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/DiagMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/FullMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/IdenMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/LowerMatrix.R                                                                   |    2 
 OpenMx-2.7.2/OpenMx/R/MxAlgebra.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxAlgebraConvert.R                                                              |    2 
 OpenMx-2.7.2/OpenMx/R/MxAlgebraFunctions.R                                                            |    2 
 OpenMx-2.7.2/OpenMx/R/MxAlgebraObjective.R                                                            |    2 
 OpenMx-2.7.2/OpenMx/R/MxAlgebraTransform.R                                                            |    2 
 OpenMx-2.7.2/OpenMx/R/MxApply.R                                                                       |    2 
 OpenMx-2.7.2/OpenMx/R/MxBounds.R                                                                      |    2 
 OpenMx-2.7.2/OpenMx/R/MxCommunication.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxCompare.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxCompute.R                                                                     |  286 ++
 OpenMx-2.7.2/OpenMx/R/MxConstraint.R                                                                  |   26 
 OpenMx-2.7.2/OpenMx/R/MxCycleDetection.R                                                              |    9 
 OpenMx-2.7.2/OpenMx/R/MxData.R                                                                        |  117 
 OpenMx-2.7.2/OpenMx/R/MxDataWLS.R                                                                     |   61 
 OpenMx-2.7.2/OpenMx/R/MxDeparse.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxDependencies.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/MxDetectCores.R                                                                 |    2 
 OpenMx-2.7.2/OpenMx/R/MxDiff.R                                                                        |    2 
 OpenMx-2.7.2/OpenMx/R/MxErrorHandling.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxEval.R                                                                        |    2 
 OpenMx-2.7.2/OpenMx/R/MxExpectation.R                                                                 |   15 
 OpenMx-2.7.2/OpenMx/R/MxExpectationBA81.R                                                             |   66 
 OpenMx-2.7.2/OpenMx/R/MxExpectationGREML.R                                                            |    7 
 OpenMx-2.7.2/OpenMx/R/MxExpectationLISREL.R                                                           |   12 
 OpenMx-2.7.2/OpenMx/R/MxExpectationNormal.R                                                           |  172 +
 OpenMx-2.7.2/OpenMx/R/MxExpectationRAM.R                                                              |   16 
 OpenMx-2.7.2/OpenMx/R/MxExpectationStateSpace.R                                                       |   54 
 OpenMx-2.7.2/OpenMx/R/MxFIMLObjective.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxFactorScores.R                                                                |  113 
 OpenMx-2.7.2/OpenMx/R/MxFitFunction.R                                                                 |    2 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionAlgebra.R                                                          |    2 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionGREML.R                                                            |    2 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionML.R                                                               |   19 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionR.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionRow.R                                                              |    2 
 OpenMx-2.7.2/OpenMx/R/MxFitFunctionWLS.R                                                              |   42 
 OpenMx-2.7.2/OpenMx/R/MxFlatModel.R                                                                   |    2 
 OpenMx-2.7.2/OpenMx/R/MxFlatSearchReplace.R                                                           |    2 
 OpenMx-2.7.2/OpenMx/R/MxGraph.R                                                                       |    2 
 OpenMx-2.7.2/OpenMx/R/MxGraphviz.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/MxInterval.R                                                                    |   57 
 OpenMx-2.7.2/OpenMx/R/MxLISRELModel.R                                                                 |    2 
 OpenMx-2.7.2/OpenMx/R/MxLISRELObjective.R                                                             |    2 
 OpenMx-2.7.2/OpenMx/R/MxMI.R                                                                          |    5 
 OpenMx-2.7.2/OpenMx/R/MxMLObjective.R                                                                 |    2 
 OpenMx-2.7.2/OpenMx/R/MxMatrix.R                                                                      |    2 
 OpenMx-2.7.2/OpenMx/R/MxMatrixFunctions.R                                                             |    2 
 OpenMx-2.7.2/OpenMx/R/MxModel.R                                                                       |   12 
 OpenMx-2.7.2/OpenMx/R/MxModelDisplay.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/MxModelFunctions.R                                                              |    2 
 OpenMx-2.7.2/OpenMx/R/MxModelParameters.R                                                             |    3 
 OpenMx-2.7.2/OpenMx/R/MxMultiModel.R                                                                  |    2 
 OpenMx-2.7.2/OpenMx/R/MxNamespace.R                                                                   |    3 
 OpenMx-2.7.2/OpenMx/R/MxObjectiveMetaData.R                                                           |    2 
 OpenMx-2.7.2/OpenMx/R/MxOptions.R                                                                     |   10 
 OpenMx-2.7.2/OpenMx/R/MxPath.R                                                                        |    2 
 OpenMx-2.7.2/OpenMx/R/MxRAMMetaData.R                                                                 |    2 
 OpenMx-2.7.2/OpenMx/R/MxRAMModel.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/MxRAMObjective.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/MxRAMtoML.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxRObjective.R                                                                  |    2 
 OpenMx-2.7.2/OpenMx/R/MxRename.R                                                                      |    2 
 OpenMx-2.7.2/OpenMx/R/MxReservedNames.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxRestore.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxRobustSE.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/MxRowObjective.R                                                                |    2 
 OpenMx-2.7.2/OpenMx/R/MxRun.R                                                                         |   58 
 OpenMx-2.7.2/OpenMx/R/MxRunHelperFunctions.R                                                          |   74 
 OpenMx-2.7.2/OpenMx/R/MxSE.R                                                                          |only
 OpenMx-2.7.2/OpenMx/R/MxSaturatedModel.R                                                              |    5 
 OpenMx-2.7.2/OpenMx/R/MxSearchReplace.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxSquareBracket.R                                                               |    2 
 OpenMx-2.7.2/OpenMx/R/MxSummary.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/MxSwift.R                                                                       |    2 
 OpenMx-2.7.2/OpenMx/R/MxThreshold.R                                                                   |    4 
 OpenMx-2.7.2/OpenMx/R/MxTryHard.R                                                                     |   44 
 OpenMx-2.7.2/OpenMx/R/MxTypes.R                                                                       |    2 
 OpenMx-2.7.2/OpenMx/R/MxUnitTesting.R                                                                 |   14 
 OpenMx-2.7.2/OpenMx/R/MxUntitled.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/MxVersion.R                                                                     |    2 
 OpenMx-2.7.2/OpenMx/R/OriginalMx.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/StandMatrix.R                                                                   |    2 
 OpenMx-2.7.2/OpenMx/R/SymmMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/UnitMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/ZeroMatrix.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/cache.R                                                                         |    2 
 OpenMx-2.7.2/OpenMx/R/omxBrownie.R                                                                    |    2 
 OpenMx-2.7.2/OpenMx/R/omxConstrainThresholds.R                                                        |    2 
 OpenMx-2.7.2/OpenMx/R/omxGetNPSOL.R                                                                   |    2 
 OpenMx-2.7.2/OpenMx/R/sysdata.rda                                                                     |binary
 OpenMx-2.7.2/OpenMx/R/zzz.R                                                                           |   10 
 OpenMx-2.7.2/OpenMx/cleanup                                                                           |only
 OpenMx-2.7.2/OpenMx/configure                                                                         |   34 
 OpenMx-2.7.2/OpenMx/data/HS.ability.data.txt.gz                                                       |binary
 OpenMx-2.7.2/OpenMx/demo/AlternativeApproaches.R                                                      |   16 
 OpenMx-2.7.2/OpenMx/demo/BivariateCorrelation.R                                                       |    2 
 OpenMx-2.7.2/OpenMx/demo/BivariateHeterogeneity_MatrixRaw.R                                           |    2 
 OpenMx-2.7.2/OpenMx/demo/BivariateHeterogeneity_PathRaw.R                                             |    2 
 OpenMx-2.7.2/OpenMx/demo/BivariateSaturated.R                                                         |    2 
 OpenMx-2.7.2/OpenMx/demo/BivariateSaturated_MatrixCov.R                                               |    2 
 OpenMx-2.7.2/OpenMx/demo/BivariateSaturated_MatrixCovCholesky.R                                       |    2 
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 OpenMx-2.7.2/OpenMx/demo/DefinitionMeans_PathRaw.R                                                    |    2 
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 OpenMx-2.7.2/OpenMx/demo/GrowthMixtureModel_PathRaw.R                                                 |    2 
 OpenMx-2.7.2/OpenMx/demo/LISRELJointFactorModel.R                                                     |   16 
 OpenMx-2.7.2/OpenMx/demo/LatentGrowthCurveModel_MatrixRaw.R                                           |    6 
 OpenMx-2.7.2/OpenMx/demo/LatentGrowthCurveModel_PathRaw.R                                             |    6 
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 OpenMx-2.7.2/OpenMx/demo/MatrixAlgebra.R                                                              |    2 
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 OpenMx-2.7.2/OpenMx/demo/MultipleRegression_MatrixRaw.R                                               |    2 
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 OpenMx-2.7.2/OpenMx/demo/MultipleRegression_PathRaw.R                                                 |    2 
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 OpenMx-2.7.2/OpenMx/demo/OneFactorJoint_MatrixRawRAM.R                                                |   36 
 OpenMx-2.7.2/OpenMx/demo/OneFactorJoint_PathRaw.R                                                     |   40 
 OpenMx-2.7.2/OpenMx/demo/OneFactorMatrixDemo.R                                                        |    2 
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 OpenMx-2.7.2/OpenMx/demo/OneFactorModel_MatrixCov.R                                                   |    6 
 OpenMx-2.7.2/OpenMx/demo/OneFactorModel_MatrixRaw.R                                                   |    6 
 OpenMx-2.7.2/OpenMx/demo/OneFactorModel_PathCov.R                                                     |    6 
 OpenMx-2.7.2/OpenMx/demo/OneFactorModel_PathRaw.R                                                     |    6 
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 OpenMx-2.7.2/OpenMx/demo/OneFactorOrdinal_MatrixRaw.R                                                 |    4 
 OpenMx-2.7.2/OpenMx/demo/OneFactorOrdinal_MatrixRawRAM.R                                              |    4 
 OpenMx-2.7.2/OpenMx/demo/OneFactorOrdinal_PathRaw.R                                                   |    4 
 OpenMx-2.7.2/OpenMx/demo/OneFactorPathDemo.R                                                          |    2 
 OpenMx-2.7.2/OpenMx/demo/OneLocusLikelihood.R                                                         |    2 
 OpenMx-2.7.2/OpenMx/demo/RObjectiveLISRELFactorRegression.R                                           |    2 
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 OpenMx-2.7.2/OpenMx/demo/SimpleCheckpoint.R                                                           |    2 
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 OpenMx-2.7.2/OpenMx/demo/SimpleRegression_MatrixRaw.R                                                 |    2 
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 OpenMx-2.7.2/OpenMx/demo/SimpleRegression_PathRaw.R                                                   |    2 
 OpenMx-2.7.2/OpenMx/demo/TwoFactorModel_MatrixCov.R                                                   |    6 
 OpenMx-2.7.2/OpenMx/demo/TwoFactorModel_MatrixRaw.R                                                   |    6 
 OpenMx-2.7.2/OpenMx/demo/TwoFactorModel_PathCov.R                                                     |    6 
 OpenMx-2.7.2/OpenMx/demo/TwoFactorModel_PathRaw.R                                                     |    6 
 OpenMx-2.7.2/OpenMx/demo/TwoLocusLikelihood.R                                                         |    2 
 OpenMx-2.7.2/OpenMx/demo/UnivariateSaturated.R                                                        |    2 
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 OpenMx-2.7.2/OpenMx/demo/mxThreshold.R                                                                |   16 
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 OpenMx-2.7.2/OpenMx/inst/CITATION                                                                     |    6 
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 OpenMx-2.7.2/OpenMx/inst/models/nightly/fm-example2-8.R                                               |    2 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/ifa-2d-mg.R                                                   |    2 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/ifa-bifactor.R                                                |    3 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/ifa-drm-wide.R                                                |    2 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/mplus-ex9.1.R                                                 |    2 
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 OpenMx-2.7.2/OpenMx/inst/models/nightly/univACErSEM.R                                                 |    6 
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 OpenMx-2.7.2/OpenMx/inst/models/nightly/xxm-hcfa.R                                                    |    2 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/xxm-lgc.R                                                     |    2 
 OpenMx-2.7.2/OpenMx/inst/models/nightly/xxm-mlcfa.R                                                   |   23 
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 OpenMx-2.7.2/OpenMx/inst/models/passing/BootstrapParallel.R                                           |    2 
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 OpenMx-2.7.2/OpenMx/inst/models/passing/FourAAAA.R                                                    |    2 
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 OpenMx-2.7.2/OpenMx/inst/models/passing/univSatM.R                                                    |    2 
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 OpenMx-2.7.2/OpenMx/man/omxAllInt.Rd                                                                  |    2 
 OpenMx-2.7.2/OpenMx/man/omxApply.Rd                                                                   |    2 
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 OpenMx-2.7.2/OpenMx/man/omxLapply.Rd                                                                  |    2 
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 OpenMx-2.7.2/OpenMx/man/omxSapply.Rd                                                                  |    2 
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 OpenMx-2.7.2/OpenMx/man/omxSetParameters.Rd                                                           |    2 
 OpenMx-2.7.2/OpenMx/man/rvectorize.Rd                                                                 |    2 
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 OpenMx-2.7.2/OpenMx/man/tr.Rd                                                                         |    2 
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 OpenMx-2.7.2/OpenMx/src/omxAlgebraFitFunction.cpp                                                     |    8 
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 OpenMx-2.7.2/OpenMx/src/omxCsolnp.h                                                                   |    9 
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 OpenMx-2.7.2/OpenMx/src/omxData.h                                                                     |   69 
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 OpenMx-2.7.2/OpenMx/src/omxExportBackendState.cpp                                                     |   10 
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 OpenMx-2.7.2/OpenMx/src/omxFitFunction.cpp                                                            |  108 
 OpenMx-2.7.2/OpenMx/src/omxFitFunction.h                                                              |   18 
 OpenMx-2.7.2/OpenMx/src/omxFitFunctionBA81.cpp                                                        |   64 
 OpenMx-2.7.2/OpenMx/src/omxGREMLExpectation.cpp                                                       |   47 
 OpenMx-2.7.2/OpenMx/src/omxGREMLExpectation.h                                                         |    3 
 OpenMx-2.7.2/OpenMx/src/omxGREMLfitfunction.cpp                                                       |  756 ++++--
 OpenMx-2.7.2/OpenMx/src/omxGREMLfitfunction.h                                                         |   27 
 OpenMx-2.7.2/OpenMx/src/omxHessianCalculation.cpp                                                     |   25 
 OpenMx-2.7.2/OpenMx/src/omxImportFrontendState.cpp                                                    |   66 
 OpenMx-2.7.2/OpenMx/src/omxLISRELExpectation.cpp                                                      |    7 
 OpenMx-2.7.2/OpenMx/src/omxLISRELExpectation.h                                                        |    2 
 OpenMx-2.7.2/OpenMx/src/omxMLFitFunction.cpp                                                          |   54 
 OpenMx-2.7.2/OpenMx/src/omxMatrix.cpp                                                                 |   70 
 OpenMx-2.7.2/OpenMx/src/omxMatrix.h                                                                   |  104 
 OpenMx-2.7.2/OpenMx/src/omxNPSOLSpecific.cpp                                                          |  231 +
 OpenMx-2.7.2/OpenMx/src/omxNPSOLSpecific.h                                                            |    2 
 OpenMx-2.7.2/OpenMx/src/omxNormalExpectation.cpp                                                      |    6 
 OpenMx-2.7.2/OpenMx/src/omxNormalExpectation.h                                                        |    2 
 OpenMx-2.7.2/OpenMx/src/omxRAMExpectation.cpp                                                         |  186 -
 OpenMx-2.7.2/OpenMx/src/omxRFitFunction.cpp                                                           |   11 
 OpenMx-2.7.2/OpenMx/src/omxRFitFunction.h                                                             |    2 
 OpenMx-2.7.2/OpenMx/src/omxRowFitFunction.cpp                                                         |   46 
 OpenMx-2.7.2/OpenMx/src/omxRowFitFunction.h                                                           |   28 
 OpenMx-2.7.2/OpenMx/src/omxSadmvnWrapper.h                                                            |  508 +++-
 OpenMx-2.7.2/OpenMx/src/omxState.cpp                                                                  |  214 +
 OpenMx-2.7.2/OpenMx/src/omxState.h                                                                    |  111 
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 OpenMx-2.7.2/OpenMx/src/omxStateSpaceExpectation.h                                                    |    5 
 OpenMx-2.7.2/OpenMx/src/omxSymbolTable.cpp                                                            |    6 
 OpenMx-2.7.2/OpenMx/src/omxSymbolTable.h                                                              |    6 
 OpenMx-2.7.2/OpenMx/src/omxWLSFitFunction.cpp                                                         |  460 ++-
 OpenMx-2.7.2/OpenMx/src/ssMLFit.cpp                                                                   |only
 OpenMx-2.7.2/OpenMx/src/subnp.cpp                                                                     |   48 
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Permanent link

New package NetworkRiskMeasures with initial version 0.1.1
Package: NetworkRiskMeasures
Type: Package
Title: Risk Measures for (Financial) Networks
Version: 0.1.1
Author: Carlos Cinelli <carloscinelli@hotmail.com>, Thiago Cristiano Silva <thiagochris@gmail.com>
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Description: Implements some risk measures for (financial) networks, such as DebtRank, Impact Susceptibility, Impact Diffusion and Impact Fluidity.
License: GPL-3
LazyData: TRUE
Suggests: testthat, igraph
Depends: Matrix
Imports: expm, ggplot2, dplyr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-10 16:51:12 UTC; carloscinelli
Repository: CRAN
Date/Publication: 2017-01-10 19:03:53

More information about NetworkRiskMeasures at CRAN
Permanent link

New package MODIS with initial version 1.0.0
Package: MODIS
Type: Package
Title: Acquisition and Processing of MODIS Products
Version: 1.0.0
Date: 2016-12-16
Authors@R: c( person("Matteo", "Mattiuzzi", role = c("cre", "aut"), email = "matteo@mattiuzzi.com"), person("Jan", "Verbesselt", role = "ctb"), person("Tomislav", "Hengl", role = "ctb"), person("Anja", "Klisch", role = "ctb"), person("Forrest", "Stevens", role = "ctb"), person("Steven", "Mosher", role = "ctb"), person("Bradley", "Evans", role = "ctb"), person("Agustin", "Lobo", role = "ctb"), person("Koen", "Hufkens", role = "ctb"), person("Florian", "Detsch", role = "ctb"))
Maintainer: Matteo Mattiuzzi <matteo@mattiuzzi.com>
Description: Download and processing functionalities for the Moderate Resolution Imaging Spectroradiometer (MODIS). The package provides automated access to the global online data archives (LPDAAC and LAADS) and processing capabilities such as file conversion, mosaicking, subsetting and time series filtering.
License: GPL (>= 3) | file LICENSE
LazyData: TRUE
Depends: mapdata, R (>= 2.10), raster
Imports: bitops, grDevices, graphics, maps, methods, parallel, ptw, RCurl, rgdal, rgeos, sp, stats, utils, XML
URL: https://github.com/MatMatt/MODIS
ByteCompile: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-10 11:22:43 UTC; fdetsch
Author: Matteo Mattiuzzi [cre, aut], Jan Verbesselt [ctb], Tomislav Hengl [ctb], Anja Klisch [ctb], Forrest Stevens [ctb], Steven Mosher [ctb], Bradley Evans [ctb], Agustin Lobo [ctb], Koen Hufkens [ctb], Florian Detsch [ctb]
Repository: CRAN
Date/Publication: 2017-01-10 18:42:37

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Package milr updated to version 0.2.0 with previous version 0.1.0 dated 2016-07-14

Title: Multiple-Instance Logistic Regression with LASSO Penalty
Description: The multiple instance data set consists of many independent subjects (called bags) and each subject is composed of several components (called instances). The outcomes of such data set are binary or multinomial, and, we can only observe the subject-level outcomes. For example, in manufactory processes, a subject is labeled as "defective" if at least one of its own components is defective, and otherwise, is labeled as "non-defective". The 'milr' package focuses on the predictive model for the multiple instance data set with binary outcomes and performs the maximum likelihood estimation with the Expectation-Maximization algorithm under the framework of logistic regression. Moreover, the LASSO penalty is attached to the likelihood function for simultaneous parameter estimation and variable selection.
Author: Ping-Yang Chen [aut, cre], ChingChuan Chen [aut], Chun-Hao Yang [aut], Sheng-Mao Chang [aut]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>

Diff between milr versions 0.1.0 dated 2016-07-14 and 0.2.0 dated 2017-01-10

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Package MEGENA updated to version 1.3.6 with previous version 1.3.5-2 dated 2016-10-25

Title: Multiscale Clustering of Geometrical Network
Description: Co-Expression Network Analysis by adopting network embedding technique.
Author: Won-Min Song, Bin Zhang
Maintainer: Won-Min Song <wonmin1984@gmail.com>

Diff between MEGENA versions 1.3.5-2 dated 2016-10-25 and 1.3.6 dated 2017-01-10

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New package CampaR1 with initial version 0.8.4
Package: CampaR1
Type: Package
Title: Trajectory Analysis
Version: 0.8.4
Date: 2016-12-20
Author: Garolini Davide
Maintainer: Garolini Davide <d.garolini@bioc.uzh.ch>
Description: Analysis algorithms extracted from the original 'campari' software package. They consists in a kinetic annotation of the trajectory based on the minimum spanning tree constructed on the distances between snapshots. The fast algorithm is implemented on the basis of a modified version of the birch algorithm, while the slow one is based on a simple leader clustering. For more information please visit the original documentation on <http://campari.sourceforge.net/index.html>.
License: GPL (>= 3)
Depends: R (>= 3.1.0)
Imports: bio3d, ggplot2
LazyData: true
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: yes
URL: https://github.com/Melkiades/CampaR1, http://campari.sourceforge.net/index.html
BugReports: https://github.com/Melkiades/CampaR1/issues
Packaged: 2017-01-10 16:33:09 UTC; dgarolini
Repository: CRAN
Date/Publication: 2017-01-10 19:03:50

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Package VGAMdata updated to version 1.0-3 with previous version 1.0-2 dated 2016-05-31

Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology).
Author: Thomas Yee [aut, cre, cph], James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

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Package sjPlot updated to version 2.2.1 with previous version 2.2.0 dated 2016-12-27

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. This package supports labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 2.2.0 dated 2016-12-27 and 2.2.1 dated 2017-01-10

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New package sitree with initial version 0.1-0
Package: sitree
Version: 0.1-0
Date: 2017-01-09
Title: Single Tree Simulator
Authors@R: c(person("Clara", "Anton Fernandez", role = c("aut", "cre"), email = "caf@nibio.no"), person("Nikolas", "von Lupke", role = "ctb"))
Author: Clara Anton Fernandez [aut, cre], Nikolas von Lupke [ctb]
Maintainer: Clara Anton Fernandez <caf@nibio.no>
Depends: R (>= 3.1.0), data.table, methods
Suggests: knitr, lattice
VignetteBuilder: knitr
Description: Forecasts plots at tree level.
License: GPL (>= 2)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2017-01-10 09:57:08 UTC; clara
Repository: CRAN
Date/Publication: 2017-01-10 15:32:34

More information about sitree at CRAN
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Package numbers updated to version 0.6-6 with previous version 0.6-1 dated 2015-07-14

Title: Number-Theoretic Functions
Description: Provides number-theoretic functions for factorization, prime numbers, twin primes, primitive roots, modular inverses, extended GCD, Farey series and continuous fractions. Included are some divisor functions, or Euler's Phi function and Egyptian fractions.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

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Package nanotime updated to version 0.1.0 with previous version 0.0.1 dated 2016-12-16

Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up to nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package marmap updated to version 0.9.6 with previous version 0.9.5 dated 2015-12-10

Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <http://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <http://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>

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Package icesDatras updated to version 1.2-0 with previous version 1.0-0 dated 2016-08-04

Title: DATRAS Trawl Database Web Services
Description: R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.
Author: Colin Millar [aut, cre], Scott Large [aut], Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>

Diff between icesDatras versions 1.0-0 dated 2016-08-04 and 1.2-0 dated 2017-01-10

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Package dfphase1 updated to version 1.1.0 with previous version 1.0.1 dated 2016-09-25

Title: Phase I Control Charts (with Emphasis on Distribution-Free Methods)
Description: Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution.
Author: Giovanna Capizzi and Guido Masarotto
Maintainer: Giovanna Capizzi <giovanna.capizzi@unipd.it>

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Package choroplethr updated to version 3.5.3 with previous version 3.5.2 dated 2016-03-30

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut], Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>

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Package tidyr updated to version 0.6.1 with previous version 0.6.0 dated 2016-08-12

Title: Easily Tidy Data with 'spread()' and 'gather()' Functions
Description: An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package textshape updated to version 1.0.0 with previous version 0.2.0 dated 2016-12-31

Title: Tools for Reshaping Text
Description: Tools that can be used to reshape text data.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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New package textclean with initial version 0.2.0
Package: textclean
Title: Text Cleaning Tools
Version: 0.2.0
Authors@R: c(person("Tyler", "Rinker", email = "tyler.rinker@gmail.com", role = c("aut", "cre")))
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Description: Tools to clean and process text.
Depends: R (>= 3.2.3)
Imports: qdapRegex, stringi, utils
Suggests: testthat, textshape, lexicon
Date: 2017-01-09
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-10 02:49:59 UTC; Tyler
Author: Tyler Rinker [aut, cre]
Repository: CRAN
Date/Publication: 2017-01-10 10:17:49

More information about textclean at CRAN
Permanent link

Package quanteda updated to version 0.9.9-3 with previous version 0.9.8.5 dated 2016-10-31

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre], Paul Nulty [ctb], Kohei Watanabe [ctb], Adam Obeng [ctb], Haiyan Wang [ctb], Benjamin Lauderdale [ctb], Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package expint updated to version 0.1-3 with previous version 0.1-2 dated 2016-12-23

Title: Exponential Integral and Incomplete Gamma Function
Description: The exponential integrals E_1(x), E_2(x), E_n(x) and Ei(x), and the incomplete gamma function G(a, x) defined for negative values of its first argument. The package also gives easy access to the underlying C routines through an API; see the package vignette for details. A test package included in sub-directory example_API provides an implementation. C routines derived from the GNU Scientific Library <https://www.gnu.org/software/gsl/>.
Author: Vincent Goulet [cre, aut], Gerard Jungman [aut] (Original GSL code), Brian Gough [aut] (Original GSL code), Jeffrey A. Ryan [aut] (Package API), Robert Gentleman [aut] (Parts of the R to C interface), Ross Ihaka [aut] (Parts of the R to C interface), R Core Team [aut] (Parts of the R to C interface), R Foundation [aut] (Parts of the R to C interface)
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

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Package ENMeval updated to version 0.2.2 with previous version 0.2.1 dated 2016-01-04

Title: Automated Runs and Evaluations of Ecological Niche Models
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006)<doi:10.1016/j.ecolmodel.2005.03.026>.
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella <bob.muscarella@gmail.com>

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Package edgar updated to version 1.0.8 with previous version 1.0.7 dated 2016-12-16

Title: Platform for EDGAR Filing Management
Description: In the USA, firms file different forms with the U.S. Securities and Exchange Commission (SEC) through EDGAR (Electronic Data Gathering, Analysis, and Retrieval system). EDGAR automated system collects all the different necessary filings and make it publicly available. Secondly, it validates collected filings, then perform indexing and accepting of these submitted forms. Investors, regulators, and researchers often require these forms for various purposes. This package helps in data gathering, management, and visualization in this regard. It downloads SEC EDGAR quarterly master indexes, daily master indexes, and filings from SEC.org site and perform sentiment analysis of these filing.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>

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Package subprocess updated to version 0.8.0 with previous version 0.7.4 dated 2016-11-29

Title: Manage Sub-Processes in R
Description: Create and handle multiple sub-processes in R, exchange data over standard input and output streams, control their life cycle.
Author: Lukasz Bartnik [aut, cre]
Maintainer: Lukasz Bartnik <l.bartnik@gmail.com>

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