Sun, 29 Sep 2013

Package fastclime updated to version 1.2.2 with previous version 1.2.1 dated 2013-09-28

Title: A fast solver for parameterized lp problems and constrained l1 minimization approach to sparse precision matrix estimation
Description: The package "fastclime" provides a method of recover the precision matrix efficiently by applying parametric simplex method. The computation is based on a linear optimization solver. It also contains a generic LP solver and a parameterized LP solver using parametric simplex method.
Author: Haotian Pang, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang

Diff between fastclime versions 1.2.1 dated 2013-09-28 and 1.2.2 dated 2013-09-29

 DESCRIPTION             |    8 ++++----
 MD5                     |   18 +++++++++---------
 R/fastclime.R           |    4 ++--
 R/fastclime.generator.R |    4 ++--
 R/fastclime.plot.R      |    4 ++--
 R/fastclime.roc.R       |    4 ++--
 R/fastlp.R              |    4 ++--
 R/paralp.R              |    4 ++--
 inst/doc/vignette.pdf   |binary
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 10 files changed, 27 insertions(+), 27 deletions(-)

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Package TSzip updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extension to connect to zip files
Description: Provides TSdbi package methods to retrieve time series data from zipped, as if the files form a database. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSzip versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION |   26 +++++++++++---------------
 MD5         |    7 ++++---
 NAMESPACE   |    3 +++
 NEWS        |    8 ++++++++
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 5 files changed, 26 insertions(+), 18 deletions(-)

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Package TSxls updated to version 2013.8-2 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extension to connect to spreadsheets
Description: Provides TSdbi package methods to retrieve time series data from spreadsheets, pretending the spreadsheet is a database. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSxls versions 2012.8-1 dated 2012-10-01 and 2013.8-2 dated 2013-09-29

 DESCRIPTION         |   25 +++++++++++--------------
 MD5                 |   11 ++++++-----
 NAMESPACE           |    3 +++
 NEWS                |   12 ++++++++++++
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 7 files changed, 46 insertions(+), 27 deletions(-)

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Package TSSQLite updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extensions for SQLite
Description: TSSQLite provides a SQLite interface for TSdbi. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSSQLite versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION         |   21 +++++++++------------
 MD5                 |   14 ++++++++------
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New package TSsql with initial version 2013.9-1
Package: TSsql
Version: 2013.9-1
Title: Generic SQL helper functions for TSdbi SQL plugins
Description: This package provides standard SQL query functions used by SQL plugins packages for the TSdbi interface to time series databases. It will mainly be used by other packages rather than directly by end users. The one exception is the function TSquery which can be used to construct a time series from a database containing observations over time (e.g. balance statements for muliple years), but where the database is not specifically designed to store time series (as with other TSdbi SQL plugin packages). Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Depends: R (>= 2.8.0)
Imports: methods, DBI, tframe (>= 2008.5-1), TSdbi (>= 2013.9-1)
Suggests: zoo, tseries, tis, tfplot, tframePlus, RMySQL, RSQLite
BuildVignettes: true
License: GPL-2
Copyright: 2007-2011 Bank of Canada. 2012-2013 Paul Gilbert.
Author: Paul Gilbert
Maintainer: Paul Gilbert
URL: http://tsdbi.r-forge.r-project.org/
Packaged: 2013-09-25 14:19:42 UTC; paul
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-29 18:08:48

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Package TSPostgreSQL updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extensions for PostgreSQL
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSPostgreSQL versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION         |   19 ++++++++-----------
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Package TSodbc updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extensions for ODBC
Description: TSodbc provides an ODBC interface for TSdbi. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSodbc versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION         |   22 +++++++++-------------
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Package TSMySQL updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-02

Title: TSdbi extensions for MySQL
Description: TSMySQL provides a MySQL interface for TSdbi. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSMySQL versions 2012.8-1 dated 2012-10-02 and 2013.9-1 dated 2013-09-29

 DESCRIPTION         |   18 +++++++++---------
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Package TShistQuote updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extensions for get.hist.quote
Description: Provides methods for generics in the TSdbi package to retrieve data from historical quote URLs. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TShistQuote versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION      |   23 ++++++++++-------------
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 NAMESPACE        |   10 ++++++++--
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New package TSjson with initial version 2013.9-1
Package: TSjson
Version: 2013.9-1
Title: TSdbi extension for importing time series from web sources via JSON
Description: Provides methods for generics in the TSdbi package to retrieve data from web data sources, importing them using Javascript object notation. Direct connections or a proxy connection are possible. (Only Statistics Canada connections are currently supported.) Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Depends: R (>= 2.14.0), TSdbi (>= 2012.8-1)
Imports: methods, DBI, tframe (>= 2011.11-1), tframePlus, rjson
Suggests: tfplot, zoo
SystemRequirements: python 2, python-sys, python-json, python-mechanize, python-re, python-csv, python-urllib2
BuildVignettes: FALSE
License: GPL-2
Author: Paul Gilbert
Maintainer: Paul Gilbert
URL: http://tsdbi.r-forge.r-project.org/
Packaged: 2013-09-25 14:43:23 UTC; paul
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-29 18:08:46

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Package TSgetSymbol updated to version 2013.9-1 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extension to connect with getSymbols
Description: Provides methods for generics in the TSdbi package to retrieve data with getSymbols, in particular from the Federal Reserve FRED database. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSgetSymbol versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29

 DESCRIPTION      |   27 ++++++++++++---------------
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Package TSfame updated to version 2013.8-2 with previous version 2012.8-1 dated 2012-10-01

Title: TSdbi extensions for fame
Description: TSfame provides a fame interface for TSdbi. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSfame versions 2012.8-1 dated 2012-10-01 and 2013.8-2 dated 2013-09-29

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Package TSdbi updated to version 2013.9-1 with previous version 2013.3-1 dated 2013-03-28

Title: TSdbi (Time Series Database Interface)
Description: TSdbi provides a common interface to time series databases. The objective is to define a standard interface so users can retrieve time series data from various sources with a simple, common, set of commands, and so programs can be written to be portable with respect to the data source. The SQL implementations also provide a database table design, so users needing to set up a time series database have a reasonably complete way to do this easily. The interface provides for a variety of options with respect to the representation of time series in R. The interface, and the SQL implementations, also handle vintages of time series data (sometime called editions or realtime data). There is also a (not yet well tested) mechanism to handle multilingual data documentation. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSdbi versions 2013.3-1 dated 2013-03-28 and 2013.9-1 dated 2013-09-29

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Package TSdata updated to version 2013.9-1 with previous version 2012.10-1 dated 2012-10-04

Title: TSdbi Illustration
Description: TSdata illustrates the various TSdbi packages using time series data from several sources. It also illustrates some simple time series manipulation and plotting using packages tframe and tfplot.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TSdata versions 2012.10-1 dated 2012-10-04 and 2013.9-1 dated 2013-09-29

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Package TScompare updated to version 2013.9-1 with previous version 2013.3-1 dated 2013-03-28

Title: TSdbi Comparison
Description: Utilities for comparing the equality of series on two databases. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between TScompare versions 2013.3-1 dated 2013-03-28 and 2013.9-1 dated 2013-09-29

 DESCRIPTION |   26 +++++++++++---------------
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Package pbdPROF updated to version 0.2-0 with previous version 0.1-0 dated 2013-08-01

Title: Programming with Big Data --- MPI Profiling Tools
Description: MPI profiling tools.
Author: Wei-Chen Chen [aut, cre], Drew Schmidt [aut], Gaurav Sehrawat [aut], Pragneshkumar Patel [aut], George Ostrouchov [aut]
Maintainer: Wei-Chen Chen

Diff between pbdPROF versions 0.1-0 dated 2013-08-01 and 0.2-0 dated 2013-09-29

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Package movMF updated to version 0.1-2 with previous version 0.1-1 dated 2013-06-19

Title: Mixtures of von Mises-Fisher Distributions
Description: Fit and simulate mixtures of von Mises-Fisher distributions.
Author: Kurt Hornik [aut, cre], Bettina GrĂ¼n [aut]
Maintainer: Kurt Hornik

Diff between movMF versions 0.1-1 dated 2013-06-19 and 0.1-2 dated 2013-09-29

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Package coloc updated to version 2.3-1 with previous version 2.3 dated 2013-09-25

Title: Colocalisation tests of two genetic traits
Description: Performs the colocalisation tests described in Plagnol et al (2009), Wallace et al (2013) and Giambartolomei et al (2013).
Author: Chris Wallace [aut, cre], Claudia Giambartolomei [aut], Vincent Plagnol [ctb]
Maintainer: Chris Wallace

Diff between coloc versions 2.3 dated 2013-09-25 and 2.3-1 dated 2013-09-29

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Package RcppArmadillo updated to version 0.3.920.1 with previous version 0.3.910.0 dated 2013-08-15

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 3.920.1). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.3.910.0 dated 2013-08-15 and 0.3.920.1 dated 2013-09-29

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Permanent link

Package Rcpp updated to version 0.10.5 with previous version 0.10.4 dated 2013-06-24

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library which facilitate the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Rcpp attributes provide a high-level syntax for declaring C++ functions as callable from R and automatically generating the code required to invoke them. Attributes are intended to facilitate both interactive use of C++ within R sessions as well as to support R package development. Attributes are built on top of Rcpp modules and their implementation is based on previous work in the inline package. Many examples are included, and around 872 unit tests in 422 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development should always use this Rcpp package instead. Additional documentation is available via the paper by Eddelbuettel and Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.10.4 dated 2013-06-24 and 0.10.5 dated 2013-09-29

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More information about Rcpp at CRAN
Permanent link

Package SNPRelate updated to version 0.9.18 with previous version 0.9.17 dated 2013-09-05

Title: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
Description: A High-performance computing toolset for relatedness and principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng

Diff between SNPRelate versions 0.9.17 dated 2013-09-05 and 0.9.18 dated 2013-09-29

 DESCRIPTION        |    8 ++++----
 MD5                |   10 +++++-----
 NEWS               |    5 +++++
 R/IBD.r            |    4 +++-
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 src/SNPRelate.cpp  |    2 +-
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More information about SNPRelate at CRAN
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Package seqminer updated to version 1.4 with previous version 1.3 dated 2013-09-26

Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL format) into R
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan and Dajiang Liu , with contributions of Jean-loup Gailly and Mark Adler (they wrote zlib and provide license so we include zlib source code), Julian Seward (this author wrote bzip2 and with BSD license we include bzip2 source codes) and Heng Li (this author wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan

Diff between seqminer versions 1.3 dated 2013-09-26 and 1.4 dated 2013-09-29

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 DESCRIPTION                                   |    6 -
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 src/BCFReader.cpp                             |    2 
 src/VCFExtractor.h                            |    2 
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 src/VCFInputFile.cpp                          |   15 ++--
 src/vcf2genoLoader.cpp                        |    4 -
 tests/tests.R                                 |    1 
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More information about seqminer at CRAN
Permanent link

New package elliplot with initial version 1.1.1
Package: elliplot
Type: Package
Title: Ellipse Summary Plot of Quantiles
Version: 1.1.1
Date: 2013-09-29
Author: Shinichiro Tomizono
Maintainer: Shinichiro Tomizono
Description: Correlation chart of two set (x and y) of data. Using Quantiles. Visualize the effect of factor.
License: MIT + file LICENSE
License_is_FOSS: yes
License_restricts_use: no
Packaged: 2013-09-29 02:50:33 UTC; macomini
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-29 08:04:54

More information about elliplot at CRAN
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