Tue, 02 Sep 2014

New package rsdmx with initial version 0.4-1
Package: rsdmx
Version: 0.4-1
Date: 2014-09-01
Title: Tools for reading SDMX data and metadata
Authors@R: c( person("Emmanuel", "Blondel", role = c("aut", "cre"), email = "emmanuel.blondel1@gmail.com"), person("Matthieu", "Stigler", role = c("ctb")))
Maintainer: Emmanuel Blondel
Depends: R (>= 2.15)
Imports: methods, XML (>= 3.96-1.1), RCurl, plyr
Suggests: testthat
Description: rsdmx provides a set of classes and methods to read data and metadata documents exchanged through the Statistical Data and Metadata Exchange (SDMX) framework. The package currently focuses on the SDMX XML standard format (SDMX-ML).
License: GPL (>= 2)
URL: https://github.com/opensdmx/rsdmx, http://www.sdmx.org
BugReports: https://github.com/opensdmx/rsdmx/issues
LazyLoad: yes
Collate: Class-SDMXSchema.R Class-SDMXType.R Class-SDMXStructureType.R Class-SDMXHeader.R Class-SDMX.R Class-SDMXGenericData.R Class-SDMXCompactData.R Class-SDMXMessageGroup.R Class-SDMXConcept.R Class-SDMXConceptScheme.R Class-SDMXConcepts.R Class-SDMXCode.R Class-SDMXCodelist.R Class-SDMXCodelists.R Class-SDMXDimension.R Class-SDMXTimeDimension.R Class-SDMXPrimaryMeasure.R Class-SDMXAttribute.R Class-SDMXComponents.R Class-SDMXDataStructure.R Class-SDMXDataStructures.R Class-SDMXDataStructureDefinition.R SDMXSchema-methods.R SDMXType-methods.R SDMXStructureType-methods.R SDMXHeader-methods.R SDMX-methods.R SDMXGenericData-methods.R SDMXCompactData-methods.R SDMXMessageGroup-methods.R SDMXConcept-methods.R SDMXConceptScheme-methods.R SDMXConcepts-methods.R SDMXCode-methods.R SDMXCodelist-methods.R SDMXCodelists-methods.R SDMXDimension-methods.R SDMXTimeDimension-methods.R SDMXPrimaryMeasure-methods.R SDMXAttribute-methods.R SDMXComponents-methods.R SDMXDataStructure-methods.R SDMXDataStructures-methods.R SDMXDataStructureDefinition-methods.R readSDMX.R
Packaged: 2014-09-01 21:45:12 UTC; Utilisateur
Author: Emmanuel Blondel [aut, cre], Matthieu Stigler [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-01 23:45:16

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New package nabor with initial version 0.4.2
Package: nabor
Type: Package
Title: Wraps libnabo, a fast K Nearest Neighbour library for low dimensions
Version: 0.4.2
Date: 2014-09-02
Author: Stephane Mangenat (for libnabo), Gregory Jefferis
Maintainer: Gregory Jefferis
Description: An R wrapper for libnabo, an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). libnabo has speed and space advantages over the ANN library wrapped by package RANN. nabor includes a knn function that is designed as a drop-in replacement for RANN::nn2. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.
License: BSD_3_clause + file LICENSE
Copyright: libnabo is copyright 2010--2011, Stephane Magnenat, ASL, ETHZ, Switzerland
URL: https://github.com/jefferis/nabor https://github.com/ethz-asl/libnabo
Depends: R (>= 3.0.2)
Imports: Rcpp (>= 0.11.2), methods
LinkingTo: Rcpp, RcppEigen (>= 0.3.2.2.0), BH (>= 1.54.0-4)
Suggests: testthat, RANN
Packaged: 2014-09-02 21:23:15 UTC; jefferis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-03 01:30:42

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New package iBATCGH with initial version 1.0
Package: iBATCGH
Type: Package
Title: Integrative Bayesian Analysis of Transcriptomic and CGH data
Version: 1.0
Date: 2014-09-02
Author: Alberto Cassese
Maintainer: Alberto Cassese
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression
License: GPL-2
Imports: Rcpp (>= 0.11.2), msm
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2014-09-02 21:48:30 UTC; ac43
Depends: R (>= 2.10)
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-03 01:16:38

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Package UsingR updated to version 2.0-2 with previous version 2.0-1 dated 2014-07-02

Title: Data sets, etc. for the text "Using R for Introductory Statistics", second edition
Description: A collection of data sets to accompany the textbook "Using R for Introductory Statistics," second edition.
Author: John Verzani
Maintainer: John Verzani

Diff between UsingR versions 2.0-1 dated 2014-07-02 and 2.0-2 dated 2014-09-02

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New package packrat with initial version 0.4.1
Package: packrat
Type: Package
Title: A dependency management system for projects and their R package dependencies
Version: 0.4.1
Date: 2014-09-02
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey
Description: Packrat is a tool for managing the R packages your project depends on in an isolated, portable, and reproducible way.
License: GPL-2
Depends: R (>= 3.0)
Imports: tools, utils
Suggests: testthat (>= 0.7), devtools
Enhances: knitr, BiocInstaller
URL: https://github.com/rstudio/packrat/
BugReports: https://github.com/rstudio/packrat/issues
Packaged: 2014-09-02 20:44:27 UTC; kevin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-03 01:01:17

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New package rcbalance with initial version 1.0
Package: rcbalance
Type: Package
Title: Large, sparse optimal matching with refined covariate balance
Version: 1.0
Date: 2014-08-08
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Depends: R (>= 3.0.0), MASS, plyr
License: MIT + file LICENSE
Packaged: 2014-08-28 17:53:05 UTC; sdbpimentel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-02 22:18:56

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Package easingr updated to version 1.0.1 with previous version 1.0.0 dated 2014-06-28

Title: Fetch and plot credit easing policy tool data.
Description: Forms queries to submit to the Cleveland Federal Reserve Bank web site's credit easing policy tools data site. Provides various query functions according to the easing data desired. By default the download includes easing tool weekly time series data starting January 2007. The functions return a class of type easing which contains a list of items related to the query and its graphical presentation. The list includes the time series data as an xts object. The package provides two lattice time series plots to render the data in a manner similar to the bank's own presentation.
Author: Matt Barry
Maintainer: Matt Barry

Diff between easingr versions 1.0.0 dated 2014-06-28 and 1.0.1 dated 2014-09-02

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Package DBI updated to version 0.3.0 with previous version 0.2-7 dated 2013-05-09

Title: R Database Interface
Description: A database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
Author: R Special Interest Group on Databases (R-SIG-DB)
Maintainer: ORPHANED

Diff between DBI versions 0.2-7 dated 2013-05-09 and 0.3.0 dated 2014-09-02

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Package roxygen2 updated to version 4.0.2 with previous version 4.0.1 dated 2014-05-17

Title: In-source documentation for R
Description: A Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE.
Author: Hadley Wickham [aut, cre, cph], Peter Danenberg [aut, cph], Manuel Eugster [aut, cph], RStudio [cph]
Maintainer: Hadley Wickham

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Package rNOMADS updated to version 2.0.2 with previous version 2.0.1 dated 2014-07-05

Title: An interface to the NOAA Operational Model Archive and Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman

Diff between rNOMADS versions 2.0.1 dated 2014-07-05 and 2.0.2 dated 2014-09-02

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New package rappdirs with initial version 0.3
Package: rappdirs
Type: Package
Title: Application directories: determine where to save data, caches and logs.
Version: 0.3
Authors@R: c( person("Hadley", "Wickham", email = "h.wickham@gmail.com", role = c("trl", "cre", "cph")), person("RStudio", role = "cph"), person("Sridhar", "Ratnakumar", role = "aut"), person("Trent", "Mick", role = "aut"), person("ActiveState", role = "cph", comment = "R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs"), person("Eddy", "Petrisor", role = "ctb"), person("Trevor", "Davis", role = c("trl", "aut")), person("Gabor", "Csardi", role = "ctb"), person("Gregory", "Jefferis", role = "ctb") )
Depends: R (>= 2.14), methods
Suggests: testthat, roxygen2
Description: An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's Appdirs (\url{https://github.com/ActiveState/appdirs}) to R.
BugReports: https://github.com/hadley/rappdirs/issues
URL: https://github.com/hadley/rappdirs https://github.com/ActiveState/appdirs
License: MIT + file LICENSE
Copyright: Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details.
Packaged: 2014-09-02 15:34:08 UTC; hadley
Author: Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb]
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-02 19:44:02

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New package ica with initial version 1.0-0
Package: ica
Type: Package
Title: Independent Component Analysis
Version: 1.0-0
Date: 2014-09-02
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
Description: Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
License: GPL (>= 2)
Packaged: 2014-09-02 16:26:17 UTC; Nate
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-02 19:41:15

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Package nor1mix updated to version 1.2-0 with previous version 1.1-4 dated 2013-04-19

Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Now fitting to data by ML (Maximum Likelihood) or EM estimation.
Author: Martin Mächler
Maintainer: Martin Maechler

Diff between nor1mix versions 1.1-4 dated 2013-04-19 and 1.2-0 dated 2014-09-02

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Package httr updated to version 0.5 with previous version 0.4 dated 2014-07-28

Title: Tools for working with URLs and HTTP
Description: Provides useful tools for working with HTTP. The API is based around http verbs (GET(), POST(), etc) with pluggable components to control the request (authenticate(), add_headers() and so on).
Author: Hadley Wickham [cre, aut, cph], RStudio [cph]
Maintainer: Hadley Wickham

Diff between httr versions 0.4 dated 2014-07-28 and 0.5 dated 2014-09-02

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Package enviPick updated to version 1.2 with previous version 1.0 dated 2014-07-14

Title: Peak picking for high resolution mass spectrometry data
Description: Sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.
Author: Martin Loos
Maintainer: Martin Loos

Diff between enviPick versions 1.0 dated 2014-07-14 and 1.2 dated 2014-09-02

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Permanent link

Package MIfuns (with last version 5.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2011-09-07 5.1
2011-09-06 5.0
2011-07-02 4.3.7
2011-06-05 4.3.2
2011-04-14 4.2.5
2011-02-08 4.2.2
2011-01-03 4.1.12
2010-08-31 4.0.17
2010-08-31 4.0.18
2010-08-28 4.0.16
2008-11-04 3.2.9
2008-10-20 3.2.7
2008-09-11 3.2.5

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Package synbreed updated to version 0.10-1 with previous version 0.9-7 dated 2013-08-27

Title: Framework for the analysis of genomic prediction data using R
Description: The package was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer

Diff between synbreed versions 0.9-7 dated 2013-08-27 and 0.10-1 dated 2014-09-02

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 synbreed-0.10-1/synbreed/R/plot.relationshipMatrix.r       |   18 
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Package prodlim updated to version 1.4.5 with previous version 1.4.3 dated 2014-05-01

Title: Product-limit estimation. Kaplan-Meier and Aalen-Johansson method for censored event history (survival) analysis
Description: Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds

Diff between prodlim versions 1.4.3 dated 2014-05-01 and 1.4.5 dated 2014-09-02

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Package ds updated to version 3.0 with previous version 2.0 dated 2013-07-01

Title: Descriptive Statistics
Description: The package performs various analyzes of descriptive statistics, including correlations
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold

Diff between ds versions 2.0 dated 2013-07-01 and 3.0 dated 2014-09-02

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Package HiClimR updated to version 1.1.4 with previous version 1.1.3 dated 2014-08-28

Title: Hierarchical Climate Regionalization: An Improved Hierarchical Clustering in R for Climate Regionalization
Description: HiClimR package modifies and improves hierarchical clustering in R ('hclust' function in 'stats' library), for climate regionalization. It adds a new clustering method (called, regional linkage) to the set of available methods together with several features including regridding, coarsening spatial resolution, geographic masking, data thresholds, detrending and standardization preprocessing, faster correlation function, hybrid hierarchical clustering, and cluster validation. Badr et. al (2014) describes the regionalization algorithms and data processing tools included in the package and presents a demonstration application in which the package is used to regionalize Africa on the basis of interannual precipitation variability. It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr

Diff between HiClimR versions 1.1.3 dated 2014-08-28 and 1.1.4 dated 2014-09-02

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Package StereoMorph updated to version 1.2.1 with previous version 1.2 dated 2014-08-24

Title: Stereo Camera Calibration and Reconstruction
Description: StereoMorph provides functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen

Diff between StereoMorph versions 1.2 dated 2014-08-24 and 1.2.1 dated 2014-09-02

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Package sgr updated to version 1.2 with previous version 1.1 dated 2014-06-03

Title: Sample Generation by Replacement
Description: The package for Sample Generation by Replacement simulations. The package can be used to perform fake data analysis according to the sample generation by replacement approach. It includes functions for making simple inferences about discrete/ordinal fake data. The package allows to study the implications of fake data for empirical results.
Author: Massimiliano Pastore & Luigi Lombardi
Maintainer: Massimiliano Pastore

Diff between sgr versions 1.1 dated 2014-06-03 and 1.2 dated 2014-09-02

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Package SCVA updated to version 1.1 with previous version 1.0 dated 2014-01-13

Title: Single-Case Visual Analysis
Description: A package to make graphical representations of single case data and to transform graphical displays back to raw data. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.
Author: Isis Bulte and Patrick Onghena
Maintainer: Marlies Vervloet

Diff between SCVA versions 1.0 dated 2014-01-13 and 1.1 dated 2014-09-02

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 10 files changed, 172 insertions(+), 53 deletions(-)

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Package SCRT updated to version 1.1 with previous version 1.0 dated 2014-01-13

Title: Single-Case Randomization Tests
Description: A package for designing single-case phase, alternation and multiple-baseline experiments, as well as for conducting randomization tests on data gathered by means of such designs.
Author: Isis Bulte and Patrick Onghena
Maintainer: Marlies Vervloet

Diff between SCRT versions 1.0 dated 2014-01-13 and 1.1 dated 2014-09-02

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Package mht updated to version 3.0.11 with previous version 3.00 dated 2014-04-07

Title: Multiple Hypotheses Testing For Variable Selection
Description: Multiple Hypotheses Testing For Variable Selection
Author: F.Rohart
Maintainer: F.Rohart

Diff between mht versions 3.00 dated 2014-04-07 and 3.0.11 dated 2014-09-02

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New package Frames2 with initial version 0.0.3
Package: Frames2
Type: Package
Title: Estimation in dual frame surveys
Version: 0.0.3
Date: 2013-07-17
Author: Antonio Arcos , Maria del Mar Rueda , Maria Giovanna Ranalli and David Molina
Maintainer: David Molina
Description: Point and interval estimation in dual frame surveys. In contrast to classic sampling theory, where only one sampling frame is considered, dual frame methodology assumes that there are two frames available for sampling and that, overall, they cover the entire target population. Then, two probability samples (one from each frame) are drawn and information collected is suitably combined to get estimators of the parameter of interest.
License: GPL (>= 2)
Depends: sampling
Packaged: 2014-09-02 07:51:43 UTC; David
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-02 10:52:13

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Package exactmeta updated to version 1.0-2 with previous version 1.0-1 dated 2013-11-24

Title: Exact fixed effect meta analysis
Description: Perform exact fixed effect meta analysis for rare events data without the need of artificial continuity correction.
Author: Yilei Yu and Lu Tian
Maintainer: Lu Tian

Diff between exactmeta versions 1.0-1 dated 2013-11-24 and 1.0-2 dated 2014-09-02

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Package rpg updated to version 1.2 with previous version 1.1 dated 2014-07-29

Title: Easy interface to advanced PostgreSQL features
Description: Allows ad hoc queries and reading and writing data frames to and from a database.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt

Diff between rpg versions 1.1 dated 2014-07-29 and 1.2 dated 2014-09-02

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Package R.devices updated to version 2.11.0 with previous version 2.9.2 dated 2014-05-18

Title: Unified handling of graphics devices
Description: This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.devices versions 2.9.2 dated 2014-05-18 and 2.11.0 dated 2014-09-02

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New package optrees with initial version 1.0
Package: optrees
Type: Package
Title: Optimal Trees in Weighted Graphs
Version: 1.0
Date: 2014-09-01
Authors@R: c(person("Manuel", "Fontenla", role = c("aut", "cre"), email = "manu.fontenla@gmail.com"))
Author: Manuel Fontenla [aut, cre]
Maintainer: Manuel Fontenla
Depends: R (>= 2.7.0), igraph (>= 0.7.1)
Description: Finds optimal trees in weighted graphs. In particular, this package provides solving tools for minimum cost spanning tree problems, minimum cost arborescence problems, shortest path tree problems and minimum cut tree problem.
License: GPL-3
Packaged: 2014-09-01 23:16:39 UTC; Manuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-02 06:14:11

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Mon, 01 Sep 2014

Package BayesNetDiscovery (with last version 0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-07-12 0.1

Permanent link
Package Rbitcoin updated to version 0.9.2 with previous version 0.9 dated 2014-04-18

Title: R & bitcoin integration
Description: Utilities related to Bitcoin. Unified markets API interface (bitstamp, kraken, btce, bitmarket). Both public and private API calls. Integration of data structures for all markets. Support SSL. Read Rbitcoin documentation (command: ?btc) for more information.
Author: Jan Gorecki
Maintainer: Jan Gorecki

Diff between Rbitcoin versions 0.9 dated 2014-04-18 and 0.9.2 dated 2014-09-01

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 Rbitcoin-0.9.2/Rbitcoin/man/market.api.query.bitstamp.Rd  |   98 +-
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Package multicore (with last version 0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-05-17 0.2
2011-09-07 0.1-7
2011-09-03 0.1-6
2011-03-10 0.1-5
2011-02-12 0.1-4
2009-02-03 0.1-3
2009-01-09 0.1-2
2009-01-03 0.1-1

Permanent link
New package xgboost with initial version 0.3-0
Package: xgboost
Type: Package
Title: eXtreme Gradient Boosting
Version: 0.3-0
Date: 2014-08-23
Author: Tianqi Chen , Tong He
Maintainer: Tong He
Description: This package is a R wrapper of xgboost, which is short for eXtreme Gradient Boosting. It is an efficient and scalable implementation of gradient boosting framework. The package includes efficient linear model solver and tree learning algorithm. The package can automatically do parallel computation with OpenMP, and it can be more than 10 times faster than existing gradient boosting packages such as gbm. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that user are also allowed to define there own objectives easily.
License: Apache License (== 2.0) | file LICENSE
URL: https://github.com/tqchen/xgboost
BugReports: https://github.com/tqchen/xgboost/issues
Depends: R (>= 2.0.2)
Imports: Matrix (>= 1.1-0), methods
Packaged: 2014-09-01 16:17:30 UTC; hetong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-01 19:46:58

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Package RCEIM updated to version 0.2 with previous version 0.1 dated 2013-11-25

Title: RCEIM - R Cross Entropy Inspired Method for Optimization
Description: RCEIM is a package implementing a stochastic heuristic method for performing multidimensional function optimization. The method is inspired in the Cross-Entropy Method. It does not relies on derivatives, neither imposes particularly strong requirements into the function to be optimized. Additionally, it takes profit from multicore processing to enable optimization of time-consuming functions.
Author: Alberto Krone-Martins
Maintainer: Alberto Krone-Martins

Diff between RCEIM versions 0.1 dated 2013-11-25 and 0.2 dated 2014-09-01

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Package geoBayes updated to version 0.1.3 with previous version 0.1.2 dated 2014-08-20

Title: Analysis of geostatistical data using Bayes and empirical Bayes methods
Description: This package provides functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while inference on the other parameters can be done through a full Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou , Vivekananda Roy
Maintainer: Evangelos Evangelou

Diff between geoBayes versions 0.1.2 dated 2014-08-20 and 0.1.3 dated 2014-09-01

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Package e1071 updated to version 1.6-4 with previous version 1.6-3 dated 2014-03-17

Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...
Author: David Meyer [aut, cre], Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut], Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer

Diff between e1071 versions 1.6-3 dated 2014-03-17 and 1.6-4 dated 2014-09-01

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New package descomponer with initial version 1.0
Package: descomponer
Type: Package
Title: Seasonal adjustment by frequency analysis
Version: 1.0
Date: 2014-08-07
Author: Francisco Parra
Maintainer: Francisco Parra
Description: Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
License: GPL (>= 2)
Depends: taRifx
Repository: CRAN
Packaged: 2014-09-01 16:44:26 UTC; PACO
NeedsCompilation: no
Date/Publication: 2014-09-01 19:46:56

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Package circlize updated to version 0.1.1 with previous version 0.1.0 dated 2014-08-02

Title: Circular visualization in R
Description: circlize implements circular visualization (http://circos.ca/) in R. Due to the natural born feature of R to draw statistical graphics, this package can provide a more general and flexible way to visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu

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Package rsdmx (with last version 0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-08-27 0.3

Permanent link
Package reader updated to version 1.0.4 with previous version 1.0.1 dated 2014-03-01

Title: A suite of functions to flexibly read data from files
Description: A set of functions to simplify reading data from files. The main function, reader(), should read most common R datafile types without needing any parameters except the filename. Other functions provide simple ways of handling file paths and extensions, and automatically detecting file format and structure.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper

Diff between reader versions 1.0.1 dated 2014-03-01 and 1.0.4 dated 2014-09-01

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Package RankAggreg updated to version 0.5 with previous version 0.4-3 dated 2012-07-01

Title: Weighted rank aggregation
Description: This package performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm (for small problems)
Author: Vasyl Pihur , Somnath Datta , Susmita Datta
Maintainer: Vasyl Pihur

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Package NCmisc updated to version 1.1.2 with previous version 1.1 dated 2014-02-27

Title: Miscellaneous general purpose functions
Description: A set of handy functions. Includes: versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more
Author: Nicholas Cooper
Maintainer: Nicholas Cooper

Diff between NCmisc versions 1.1 dated 2014-02-27 and 1.1.2 dated 2014-09-01

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Package lgarch updated to version 0.5 with previous version 0.4 dated 2014-07-01

Title: Simulation and estimation of log-GARCH models
Description: Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim, mlgarchSim, lgarch and mlgarch. The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively. A collection of methods can be applied to objects of both the 'lgarch' and 'mlgarch' types: coef, fitted, logLik, print, residuals, summary and vcov.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat

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Package GGIR updated to version 1.0-6 with previous version 1.0-4 dated 2014-04-29

Title: GGIR
Description: GGIR is a tool to process multi-day raw acceleration data
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb]
Maintainer: Vincent T van Hees

Diff between GGIR versions 1.0-4 dated 2014-04-29 and 1.0-6 dated 2014-09-01

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Package agricolae updated to version 1.2-1 with previous version 1.2-0 dated 2014-06-30

Title: Statistical Procedures for Agricultural Research
Description: Agricolae was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, mention Systems Engineering, Faculty of Industrial and Systems Engineering, National Engineering University (UNI), Lima-Peru. Original idea, support and data sets came from CIP (International Potato Center). Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu

Diff between agricolae versions 1.2-0 dated 2014-06-30 and 1.2-1 dated 2014-09-01

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Package Nemenyi (with last version 1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-08-18 1.2
2014-07-14 1.1
2014-05-13 1.0

Permanent link
Package wordnet updated to version 0.1-10 with previous version 0.1-9 dated 2013-07-29

Title: WordNet Interface
Description: An interface to WordNet using the Jawbone Java API to WordNet. WordNet () is a large lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing a distinct concept. Synsets are interlinked by means of conceptual-semantic and lexical relations. Please note that WordNet(R) is a registered tradename. Princeton University makes WordNet available to research and commercial users free of charge provided the terms of their license () are followed, and proper reference is made to the project using an appropriate citation ().
Author: Ingo Feinerer [aut], Kurt Hornik [aut, cre], Mike Wallace [ctb, cph] (Jawbone Java WordNet API library)
Maintainer: Kurt Hornik

Diff between wordnet versions 0.1-9 dated 2013-07-29 and 0.1-10 dated 2014-09-01

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Package traitr updated to version 0.14 with previous version 0.13 dated 2012-01-26

Title: An interface for creating GUIs modeled in part after traits UI module for python.
Description: An interface for creating GUIs modeled in part after the traits UI module for python. The basic design takes advantage of the model-view-controller design pattern. The interface makes basic dialogs quite easy to produce.
Author: John Verzani
Maintainer: John Verzani

Diff between traitr versions 0.13 dated 2012-01-26 and 0.14 dated 2014-09-01

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More information about traitr at CRAN
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New package Tampo with initial version 1.0
Package: Tampo
Type: Package
Title: Tools for the Analysis of Microchemical Profiles from Otoliths
Version: 1.0
Date: 2014-08-28
Author: Matthias Vignon
Maintainer: Matthias Vignon
Description: Facilitates analyzing microchemical profiles (both mono- and multielemental composition) from fish otoliths (stones from the inner ear) using a recursive partitioning approach that can accommodate some form of user-specified constraints. It also allows extracting environmental histories from otolith based on typical elemental sequences generated using methods such as LA-ICPMS. Microchemical analysis is widely used in fisheries management and fisheries biology to identify stocks and characterize fish movements but the provided functions may be considered from the more general perspective of the chronological clustering of multivariate time series using piecewise constant regressions.
Depends: R(>= 3.0.2), mvpart
Suggests: boot, reshape, reshape2, ggplot2, grid, ggdendro, sets, mgcv
License: GPL (>= 2)
Packaged: 2014-09-01 11:08:35 UTC; Matthias
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-01 15:47:56

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Package OpasnetUtils updated to version 1.1.0 with previous version 1.0.0 dated 2013-07-17

Title: Utility functions for dealing with data in Opasnet (www.opasnet.org) environment.
Description: This package is primarily developed for executing open assessments and modeling in Opasnet environment (http://www.opasnet.org). The operating principle of this package is maximum openness and modularity. Variables are defined publicly on wiki pages using wiki inputs/tables, our database and R code. Using any predefined variable is very easy: fetch the variable from our servers (or your own) and evaluate it. Actual evaluation of variables is done lazily by default: when the evaluation of a variable is explicitly called, all variables it is dependent on are evaluated recursively. There are also a couple of impact assessment tools such as GIS functions in the package. To learn more go to \url{http://en.opasnet.org/w/Modelling_in_Opasnet}.
Author: Teemu Rintala, Einari Happonen, Jouni Tuomisto
Maintainer: Teemu Rintala

Diff between OpasnetUtils versions 1.0.0 dated 2013-07-17 and 1.1.0 dated 2014-09-01

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Package mixOmics updated to version 5.0-3 with previous version 5.0-2 dated 2014-08-10

Title: Omics Data Integration Project
Description: The package provide statistical integrative techniques and variants to analyse highly dimensional data sets: regularized CCA and sparse PLS to unravel relationships between two heterogeneous data sets of size (nxp) and (nxq) 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 CCA 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, Independent Principal Component Analysis and multilevel analysis using variance decomposition of the data.
Author: Sebastien Dejean, Ignacio Gonzalez, Kim-Anh Le Cao with contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet, Florian Rohart
Maintainer: Kim-Anh Le Cao

Diff between mixOmics versions 5.0-2 dated 2014-08-10 and 5.0-3 dated 2014-09-01

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Package StAMPP updated to version 1.3 with previous version 1.2 dated 2014-03-10

Title: Statistical Analysis of Mixed Ploidy Populations
Description: StAMPP allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton

Diff between StAMPP versions 1.2 dated 2014-03-10 and 1.3 dated 2014-09-01

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Package freqweights updated to version 0.1.1 with previous version 0.1.0 dated 2014-05-21

Title: Working with frequency tables
Description: The frequency of a particular data value is the number of times it occurs. A frequency table is a table of values with their corresponding frequencies. Frequency weights are integer numbers that indicate how many cases each case represents. This package provides some functions to work with such type of collected data.
Author: Emilio Torres-Manzanera
Maintainer: Emilio Torres-Manzanera

Diff between freqweights versions 0.1.0 dated 2014-05-21 and 0.1.1 dated 2014-09-01

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Package FADA updated to version 1.1 with previous version 1.0 dated 2014-07-10

Title: Variable selection for supervised classification in high dimension
Description: The functions provided in the FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised classification models and variable selection on dependent covariates. The classification procedures are combined with a factor modeling of dependence among covariates. The available procedures are Lasso regularized logistic model (see Friedman et al. (2010)), sparse linear discriminant analysis (see Clemmensen et al. (2011)), shrinkage linear and diagonal discriminant analysis (see M. Ahdesmaki et al. (2010)).
Author: Emeline Perthame (Agrocampus Ouest, Rennes, France), Chloe Friguet (Universite de Bretagne Sud, Vannes, France) and David Causeur (Agrocampus Ouest, Rennes, France)
Maintainer: David Causeur

Diff between FADA versions 1.0 dated 2014-07-10 and 1.1 dated 2014-09-01

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Package chebpol updated to version 1.3-1367 with previous version 1.3-1040 dated 2013-07-28

Title: Multivariate Chebyshev interpolation
Description: The package contains methods for creating multivariate Chebyshev approximation of functions on a hypercube. Some methods for non-Chebyshev grids are also provided.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo, Norway
Maintainer: Simen Gaure

Diff between chebpol versions 1.3-1040 dated 2013-07-28 and 1.3-1367 dated 2014-09-01

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Package RGA updated to version 0.1.2 with previous version 0.1.1 dated 2014-08-20

Title: A Google Analytics API client for R
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 the RGA 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

Diff between RGA versions 0.1.1 dated 2014-08-20 and 0.1.2 dated 2014-09-01

 DESCRIPTION |    6 +++---
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New package pdR with initial version 1.1
Package: pdR
Type: Package
Title: panel data regression
Version: 1.1
Date: 2014-09-01
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu
Description: threshold regression in panel data
License: GPL (>= 2)
Packaged: 2014-09-01 08:00:01 UTC; shu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-01 10:36:12

More information about pdR at CRAN
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Package heavy updated to version 0.2-35 with previous version 0.2-3 dated 2013-03-22

Title: Package for robust estimation using heavy-tailed distributions
Description: This package contains functions to perform robust estimation considering heavy-tailed distributions. Currently, the package includes linear regression, linear mixed-effect models, multivariate location and scatter estimation, penalized splines and random variate generation.
Author: Felipe Osorio
Maintainer: Felipe Osorio

Diff between heavy versions 0.2-3 dated 2013-03-22 and 0.2-35 dated 2014-09-01

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More information about heavy at CRAN
Permanent link

Sun, 31 Aug 2014

Package RNetCDF updated to version 1.6.3-1 with previous version 1.6.2-3 dated 2014-06-16

Title: R Interface to NetCDF Datasets
Description: This package provides an interface to Unidata's NetCDF library functions (version 3) and furthermore access to Unidata's UDUNITS calendar conversions. The routines and the documentation follow the NetCDF and UDUNITS C interface, so the corresponding manuals can be consulted for more detailed information.
Author: Pavel Michna
Maintainer: Pavel Michna

Diff between RNetCDF versions 1.6.2-3 dated 2014-06-16 and 1.6.3-1 dated 2014-08-31

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Package ngramr updated to version 1.4.5 with previous version 1.4.3 dated 2014-02-01

Title: Retrieve and plot Google n-gram data
Description: Retrieve and plot word frequencies through time from the Google Ngram Viewer
Author: Sean Carmody
Maintainer: Sean Carmody

Diff between ngramr versions 1.4.3 dated 2014-02-01 and 1.4.5 dated 2014-08-31

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Package chemosensors updated to version 0.7.8 with previous version 0.7.7 dated 2013-10-09

Title: A tool for the design of synthetic experiments in machine olfaction.
Description: This package introduces a software tool for the design of synthetic experiments in machine olfaction. The generator of gas sensor signals can be used in applications related to test and benchmarking of signal processing methods, neuromorphic simulations in machine olfaction and educational tools. A so-called virtual sensor array features unlimited number of sensors, support of multicomponent gas mixtures and full parametric control of the noise in the system. The artificial (virtual) sensor array is inspired from a reference database of seventeen polymeric sensors with concentration profiles for three analytes.
Author: Alexandre Perera-Lluna and Andrey Ziyatdinov
Maintainer: Andrey Ziyatdinov

Diff between chemosensors versions 0.7.7 dated 2013-10-09 and 0.7.8 dated 2014-08-31

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Package chords updated to version 0.90 with previous version 0.67 dated 2012-09-05

Title: Estimation in respondent driven samples.
Description: Maximum likelihood estimation in respondent driven samples.
Author: Jonathan Rosenblatt
Maintainer: Jonathan Rosenblatt

Diff between chords versions 0.67 dated 2012-09-05 and 0.90 dated 2014-08-31

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Package CDM updated to version 3.4-21 with previous version 3.3-24 dated 2014-05-25

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

Diff between CDM versions 3.3-24 dated 2014-05-25 and 3.4-21 dated 2014-08-31

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 43 files changed, 1172 insertions(+), 970 deletions(-)

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New package lbfgs with initial version 1.2.1
Package: lbfgs
Type: Package
Title: Limited-memory BFGS Optimization
Version: 1.2.1
Date: 2014-07-08
Authors@R: c(person("Antonio", "Coppola", role = c("aut", "cre", "cph"), email = "acoppola@college.harvard.edu"), person("Brandon", "Stewart", role = c("aut", "cph")), person("Naoaki", "Okazaki", role = c("aut", "cph")), person("David", "Ardia", role = c("ctb", "cph")), person("Dirk", "Eddelbuettel", role = c("ctb", "cph")), person("Katharine", "Mullen", role = c("ctb", "cph")), person("Jorge", "Nocedal", role = c("ctb", "cph")))
Maintainer: Antonio Coppola
Description: A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp
Packaged: 2014-08-30 10:14:37 UTC; antonio12
Author: Antonio Coppola [aut, cre, cph], Brandon Stewart [aut, cph], Naoaki Okazaki [aut, cph], David Ardia [ctb, cph], Dirk Eddelbuettel [ctb, cph], Katharine Mullen [ctb, cph], Jorge Nocedal [ctb, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-31 11:23:32

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Package pmg updated to version 0.9-43 with previous version 0.9-42 dated 2010-03-09

Title: Poor Man's GUI
Description: Simple GUI for R using gWidgets.
Author: John Verzani with contributions by Yvonnick Noel
Maintainer: John Verzani

Diff between pmg versions 0.9-42 dated 2010-03-09 and 0.9-43 dated 2014-08-31

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New package SimuChemPC with initial version 1.3
Package: SimuChemPC
Type: Package
Title: Simulation process of 4 selection methods in predicting chemical potent compounds
Version: 1.3
Date: 2014-02-23
Author: Mohsen Ahmadi
Maintainer: Mohsen Ahmadi
Description: This package provides simulation process of 4 selection methods in predicting potent compounds
License: GPL-3
Depends: stats, graphics, grDevices, utils, rcdk, R (>= 2.13)
Packaged: 2014-02-24 22:53:35 UTC; M0H3N
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-02-25 07:44:36

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New package rcdklibs with initial version 1.5.8.4
Package: rcdklibs
Version: 1.5.8.4
Date: 2014-08-30
Title: rcdklib - CDK libraries packaged for R
Authors@R: c(person('Rajarshi', 'Guha', role=c('aut','cre'), email='rajarshi.guha@gmail.com'), person('CDK Project', '', role=c('ctb', 'cph'), comment='CDK Java library contained in multiple jar files'))
Maintainer: Rajarshi Guha
Depends: R (>= 2.0.0), rJava
License: LGPL
Description: This package provides the CDK libraries for use in the R environment. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the rcdk package. Note that it is possible to directly interact with the CDK using rJava. However rcdk exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from https://github.com/cdk/cdk
Packaged: 2014-08-30 17:36:06 UTC; guhar
Author: Rajarshi Guha [aut, cre], CDK Project [ctb, cph] (CDK Java library contained in multiple jar files)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-31 08:05:15

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New package rcdk with initial version 3.3.0
Package: rcdk
Version: 3.3.0
Date: 2014-08-30
Title: rcdk - Interface to the CDK Libraries
Authors@R: c(person('Rajarshi', 'Guha', role=c('aut','cre', 'cph'), email='rajarshi.guha@gmail.com'))
Maintainer: Rajarshi Guha
Depends: fingerprint
Imports: rJava, rcdklibs (>= 1.5.8), methods, png, iterators
Suggests: xtable, RUnit
License: LGPL
LazyLoad: yes
Description: This package allows the user to access functionality in the CDK, a Java framework for cheminformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition the CDK API allows the user to view structures in 2D.
Packaged: 2014-08-30 17:36:06 UTC; guhar
Author: Rajarshi Guha [aut, cre, cph]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-31 08:05:15

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Sat, 30 Aug 2014

Package survivalMPL updated to version 0.1.1 with previous version 0.1.0 dated 2014-04-03

Title: Penalised Maximum Likelihood for Survival Analysis Models
Description: Estimate the regression coefficients and the baseline hazard of proportional hazard Cox models using maximum penalised likelihood. A 'non-parametric' smooth estimate of the baseline hazard function is provided.
Author: Dominique-Laurent Couturier, Jun Ma, Stephane Heritier.
Maintainer: Dominique-Laurent Couturier

Diff between survivalMPL versions 0.1.0 dated 2014-04-03 and 0.1.1 dated 2014-08-30

 DESCRIPTION                |   10 +++++-----
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Package nsRFA updated to version 0.7-12 with previous version 0.7-11 dated 2013-12-16

Title: Non-supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves.
Author: Alberto Viglione [aut, cre], Jonathan R. M. Hosking [ctb], Francesco Laio [ctb], Alan Miller [ctb], Eric Gaume [ctb], Olivier Payrastre [ctb], Jose Luis Salinas [ctb], Chi Cong N'guyen [ctb], Karine Halbert [ctb]
Maintainer: Alberto Viglione

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Package jvmr updated to version 2.11.2.1 with previous version 2.11.1.1 dated 2014-06-25

Title: Integration of R, Java, and Scala
Description: Cross-platform, self-contained, and bi-directional interface between R and Scala, Java, and other JVM-based languages.
Author: David B. Dahl [aut, cre], Scala developers [ctb] (see http://scala-lang.org/), beanshell2 developers [ctb] (see https://code.google.com/p/beanshell2/), jline2 developers [ctb] (see https://github.com/jline/jline2)
Maintainer: David B. Dahl

Diff between jvmr versions 2.11.1.1 dated 2014-06-25 and 2.11.2.1 dated 2014-08-30

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Package frailtypack updated to version 2.7 with previous version 2.6.1 dated 2014-07-23

Title: General Frailty models: shared, joint and nested frailty models with prediction
Description: Frailtypack fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

Diff between frailtypack versions 2.6.1 dated 2014-07-23 and 2.7 dated 2014-08-30

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 src/joint.f90                      |  211 ++---
 src/multiveJoint.f90               |   44 -
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 95 files changed, 4826 insertions(+), 4263 deletions(-)

More information about frailtypack at CRAN
Permanent link

Package Peptides updated to version 1.0 with previous version 0.4 dated 2014-03-26

Title: Calculate indices and theoretical physicochemical properties of peptides and protein sequences
Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files .XVG.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio

Diff between Peptides versions 0.4 dated 2014-03-26 and 1.0 dated 2014-08-30

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 46 files changed, 590 insertions(+), 386 deletions(-)

More information about Peptides at CRAN
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Package parsedate updated to version 1.0.3 with previous version 1.0.2 dated 2014-08-28

Title: Recognize and parse dates in various formats, including all ISO 8601 formats
Description: Parse dates automatically, without the need of specifying a format. Currently it includes the git date parser. It can also recognize and parse all ISO 8601 formats.
Author: Gabor Csardi, Linus Torvalds
Maintainer: Gabor Csardi

Diff between parsedate versions 1.0.2 dated 2014-08-28 and 1.0.3 dated 2014-08-30

 DESCRIPTION           |    6 +++---
 MD5                   |    6 +++---
 R/parsedate-package.r |    3 +--
 tests/testthat.R      |    4 +++-
 4 files changed, 10 insertions(+), 9 deletions(-)

More information about parsedate at CRAN
Permanent link

New package archivist with initial version 1.0
Package: archivist
Version: 1.0
Type: Package
Title: Tools for storing, restoring and searching for R objects
Authors@R: c( person("Przemyslaw", "Biecek", role = c("aut", "cre"), email = "przemyslaw.biecek@gmail.com"), person("Marcin", "Kosinski", role = c("aut"), email = "m.p.kosinski@gmail.com") )
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Repository: CRAN
License: GPL-2
LazyLoad: yes
LazyData: yes
Depends: R (>= 3.0.0), RSQLite, DBI, lubridate, jsonlite
Imports: RCurl, digest, httr
BugReports: https://github.com/pbiecek/archivist/issues
Packaged: 2014-08-30 18:30:21 UTC; pbiecek
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek
NeedsCompilation: no
Date/Publication: 2014-08-30 23:00:41

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Package sirt updated to version 0.47-36 with previous version 0.46-15 dated 2014-08-05

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch

Diff between sirt versions 0.46-15 dated 2014-08-05 and 0.47-36 dated 2014-08-30

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 74 files changed, 2302 insertions(+), 1139 deletions(-)

More information about sirt at CRAN
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Package PopGenome updated to version 2.0.9 with previous version 2.0.8 dated 2014-07-31

Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer

Diff between PopGenome versions 2.0.8 dated 2014-07-31 and 2.0.9 dated 2014-08-30

 DESCRIPTION                                           |    8 
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 NEWS                                                  |   13 +
 R/PopGplot.R                                          |    4 
 R/Whop_readVCF.R                                      |   26 +--
 R/concatenate.R                                       |   24 +-
 R/fstcalc.R                                           |    4 
 R/get_gff_info.R                                      |   18 +-
 R/get_segsites.R                                      |    2 
 R/linkdisequ_FAST.R                                   |   18 +-
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 R/readVCF.R                                           |  152 ++++++++++++++----
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 man/readVCF.Rd                                        |    9 -
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 23 files changed, 466 insertions(+), 132 deletions(-)

More information about PopGenome at CRAN
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Package mcIRT updated to version 0.41 with previous version 0.40 dated 2014-03-15

Title: IRT models for multiple choice items (mcIRT)
Description: This package provides functions to estimate two popular IRT-models: The Nominal Response Model (Bock 1972) and the quite recently developed Nested Logit Model (Suh & Bolt 2010). These are two models to examine multiple-choice items and other multicategorial response formats.
Author: Manuel Reif
Maintainer: Manuel Reif

Diff between mcIRT versions 0.40 dated 2014-03-15 and 0.41 dated 2014-08-30

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 7 files changed, 52 insertions(+), 32 deletions(-)

More information about mcIRT at CRAN
Permanent link

Package TDMR updated to version 1.2 with previous version 1.1 dated 2014-06-06

Title: Tuned Data Mining in R
Description: Tuned Data Mining in R (TDMR) performs a complete tuning of a data mining task.
Author: Wolfgang Konen , Patrick Koch
Maintainer: Wolfgang Konen

Diff between TDMR versions 1.1 dated 2014-06-06 and 1.2 dated 2014-08-30

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More information about TDMR at CRAN
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Package PP updated to version 0.5 with previous version 0.2-1 dated 2013-12-29

Title: Person Parameter estimation
Description: The PP package includes estimation of (MLE, WLE, MAP, EAP, ROBUST) person parameters for the 1,2,3,4-PL model and the GPCM (generalized partial credit model). The parameters are estimated under the assumption that the item parameters are known and fixed. The package could be useful when items from an itempool/itembank with known item parameters are administered to a new population of testtakers and an ability estimation for every testtaker is needed.
Author: Manuel Reif
Maintainer: Manuel Reif

Diff between PP versions 0.2-1 dated 2013-12-29 and 0.5 dated 2014-08-30

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Package RSiteCatalyst updated to version 1.4.0 with previous version 1.3.3 dated 2014-04-12

Title: R Client for Adobe Analytics API v1.4
Description: Functions for accessing the Adobe Analytics Reporting API
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch

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Package transmission (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-06-13 0.2.0

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2012-07-22 0.2-0
2012-06-18 0.1-0

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Package transnet (with last version 0.1) was removed from CRAN

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2012-11-13 0.1

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Package EpiModel updated to version 1.0.2 with previous version 1.0.1 dated 2014-07-29

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Li Wang [ctb]
Maintainer: Samuel Jenness

Diff between EpiModel versions 1.0.1 dated 2014-07-29 and 1.0.2 dated 2014-08-30

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Package colbycol (with last version 0.8) was removed from CRAN

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2013-10-22 0.8
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2013-04-07 1.0-1
2013-04-05 1.0

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2012-07-17 0.9.5.1
2012-03-21 0.9.5
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2008-07-08 0.9
2007-02-11 0.8.4.2

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2014-06-16 1.0-0
2014-02-28 0.9-7
2013-04-25 0.9-6
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2013-01-17 0.9.4
2012-07-19 0.9.3
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2010-01-18 2.2
2009-07-01 2.1
2009-06-24 1.0

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2010-02-02 1.0-5
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Package Mobilize (with last version 2.16-2) was removed from CRAN

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2014-02-23 2.16-2
2012-07-05 2.11-2
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2012-01-13 2.9-4
2011-12-27 2.9

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Package RHmm (with last version 2.0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-04-13 2.0.3
2012-09-11 2.0.2

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Package sns updated to version 0.9.1 with previous version 0.9 dated 2014-08-25

Title: Stochastic Newton Sampler (SNS)
Description: Multivariate, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability densities. SNS is a Metropolis-Hastings variant, where the proposal function is a local Gaussian approximation to the density obtained via a second order Taylor expansion around the current point. The mean of the Gaussian proposal is taken as the full Newton-Raphson step from the current point. During burn-in, Newton-Raphson optimization is performed to get close to the mode of the pdf which is unique due to convexity.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Asad Hasan

Diff between sns versions 0.9 dated 2014-08-25 and 0.9.1 dated 2014-08-30

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New package apc with initial version 1.0
Package: apc
Type: Package
Title: Age-period-cohort analysis
Version: 1.0
Date: 2014-08-29
Author: Bent Nielsen
Maintainer: Bent Nielsen
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
License: GPL-3
Packaged: 2014-08-29 23:41:27 UTC; Nielsen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-30 06:52:00

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Fri, 29 Aug 2014

Package RcmdrPlugin.IPSUR updated to version 0.2-0 with previous version 0.1-8 dated 2012-03-23

Title: An IPSUR Plugin for the R Commander
Description: This package is an R Commander plugin that accompanies IPSUR, an Introduction to Probability and Statistics Using R.
Author: G. Jay Kerns [aut, cre], Theophilus Boye [ctb], Tyler Drombosky [ctb]
Maintainer: G. Jay Kerns

Diff between RcmdrPlugin.IPSUR versions 0.1-8 dated 2012-03-23 and 0.2-0 dated 2014-08-29

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Package mgcv updated to version 1.8-3 with previous version 1.8-2 dated 2014-07-21

Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood

Diff between mgcv versions 1.8-2 dated 2014-07-21 and 1.8-3 dated 2014-08-29

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