Wed, 20 Feb 2013

Package simctest updated to version 2.2 with previous version 2.1 dated 2012-09-17

Title: Safe implementation of Monte Carlo tests.
Description: Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
Author: Axel Gandy with contributions from Patrick Rubin-Delanchy and Georg Hahn
Maintainer: Axel Gandy

Diff between simctest versions 2.1 dated 2012-09-17 and 2.2 dated 2013-02-20

 DESCRIPTION                         |    7 ++++---
 MD5                                 |   24 ++++++++++++------------
 R/mmctest.R                         |   36 ++++++++++++++++++++++++------------
 R/simctest.R                        |    2 +-
 inst/doc/papers.bib                 |    4 ++--
 inst/doc/simctest-intro.pdf         |binary
 inst/doc/simctest-mmctest-intro.Rnw |   28 +++++++++++++++-------------
 inst/doc/simctest-mmctest-intro.pdf |binary
 man/mmctSampler-class.Rd            |    4 ++--
 man/mmctSamplerGeneric-class.Rd     |    4 ++--
 man/mmctest-class.Rd                |    4 ++--
 man/mmctest-methods.Rd              |    6 ++++--
 man/mmctestres-class.Rd             |    5 +++--
 13 files changed, 71 insertions(+), 53 deletions(-)

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Package RcppArmadillo updated to version 0.3.6.3 with previous version 0.3.6.2 dated 2013-01-30

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 3.6.3). 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 GNU LGPL version 3 or later, 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 0.3.6.2 dated 2013-01-30 and 0.3.6.3 dated 2013-02-20

 ChangeLog                                                |    6 
 DESCRIPTION                                              |   11 
 MD5                                                      |   72 +--
 inst/NEWS.Rd                                             |   11 
 inst/include/armadillo_bits/Mat_bones.hpp                |    6 
 inst/include/armadillo_bits/Mat_meat.hpp                 |   88 ++++
 inst/include/armadillo_bits/SpMat_iterators_meat.hpp     |    6 
 inst/include/armadillo_bits/SpMat_meat.hpp               |  128 ++----
 inst/include/armadillo_bits/SpSubview_bones.hpp          |    2 
 inst/include/armadillo_bits/SpSubview_iterators_meat.hpp |  112 ++---
 inst/include/armadillo_bits/SpSubview_meat.hpp           |  151 +++----
 inst/include/armadillo_bits/arma_ostream_meat.hpp        |    3 
 inst/include/armadillo_bits/arma_version.hpp             |    2 
 inst/include/armadillo_bits/diskio_meat.hpp              |    2 
 inst/include/armadillo_bits/eGlueCube_meat.hpp           |    4 
 inst/include/armadillo_bits/eGlue_meat.hpp               |    4 
 inst/include/armadillo_bits/eOpCube_meat.hpp             |    2 
 inst/include/armadillo_bits/fn_conv_to.hpp               |   12 
 inst/include/armadillo_bits/fn_eps.hpp                   |    3 
 inst/include/armadillo_bits/fn_mean.hpp                  |    2 
 inst/include/armadillo_bits/fn_misc.hpp                  |   34 +
 inst/include/armadillo_bits/fn_norm.hpp                  |    6 
 inst/include/armadillo_bits/fn_rank.hpp                  |    3 
 inst/include/armadillo_bits/fn_reshape.hpp               |    6 
 inst/include/armadillo_bits/fn_svd.hpp                   |    4 
 inst/include/armadillo_bits/glue_times_meat.hpp          |   10 
 inst/include/armadillo_bits/op_cx_scalar_meat.hpp        |  179 ++++++--
 inst/include/armadillo_bits/op_dot_meat.hpp              |   12 
 inst/include/armadillo_bits/op_find_meat.hpp             |  173 +++++---
 inst/include/armadillo_bits/op_inv_meat.hpp              |    2 
 inst/include/armadillo_bits/op_mean_meat.hpp             |    3 
 inst/include/armadillo_bits/op_var_meat.hpp              |    6 
 inst/include/armadillo_bits/running_stat_meat.hpp        |    2 
 inst/include/armadillo_bits/spop_var_meat.hpp            |    4 
 inst/include/armadillo_bits/subview_elem1_meat.hpp       |   14 
 inst/include/armadillo_bits/subview_elem2_meat.hpp       |   22 -
 inst/include/armadillo_bits/unwrap.hpp                   |  317 +++++++++++++++
 37 files changed, 988 insertions(+), 436 deletions(-)

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Package eaf updated to version 1.05 with previous version 1.04 dated 2012-01-10

Title: Plots of the Empirical Attainment Function
Description: Plots of the empirical attainment function for two objectives.
Author: Carlos Fonseca, Luis Paquete, Thomas Stützle, Manuel López-Ibáñez and Marco Chiarandini.
Maintainer: Manuel López-Ibáñez

Diff between eaf versions 1.04 dated 2012-01-10 and 1.05 dated 2013-02-20

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 30 files changed, 1954 insertions(+), 654 deletions(-)

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Package selectr updated to version 0.2-1 with previous version 0.2-0 dated 2012-11-23

Title: Translate CSS Selectors to XPath Expressions
Description: Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package "cssselect" (http://packages.python.org/cssselect/).
Author: Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]
Maintainer: Simon Potter

Diff between selectr versions 0.2-0 dated 2012-11-23 and 0.2-1 dated 2013-02-20

 DESCRIPTION                   |    9 ++++----
 MD5                           |   11 +++++-----
 R/parser.R                    |   43 +++++++++++++++++++++++++++++++++++++-----
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 inst/tests/test-translation.R |    4 ---
 7 files changed, 90 insertions(+), 31 deletions(-)

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Package microbenchmark updated to version 1.3-0 with previous version 1.1-3 dated 2011-10-19

Title: Sub microsecond accurate timing functions.
Description: Provides infrastructure to accurately measure and compare the execution time of R expressions.
Author: Olaf Mersmann
Maintainer: Olaf Mersmann

Diff between microbenchmark versions 1.1-3 dated 2011-10-19 and 1.3-0 dated 2013-02-20

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 microbenchmark-1.3-0/microbenchmark/ChangeLog                      |  106 +++-
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 26 files changed, 386 insertions(+), 447 deletions(-)

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Package arm updated to version 1.6-03 with previous version 1.6-01.02 dated 2013-01-07

Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing lm, glm, mer and polr outputs.
Author: Andrew Gelman [aut], Yu-Sung Su [aut, cre], Masanao Yajima [ctb], Jennifer Hill [ctb], Maria Grazia Pittau [ctb], Jouni Kerman [ctb] and Tian Zheng [ctb]
Maintainer: Yu-Sung Su

Diff between arm versions 1.6-01.02 dated 2013-01-07 and 1.6-03 dated 2013-02-20

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 arm-1.6-03/arm/R/AllClass.R   |    1 
 arm-1.6-03/arm/R/coefplot.R   |   43 +++++++++++++++++++++--------------------
 arm-1.6-03/arm/R/display.R    |   44 ++++++++++++++++++++++++++++++++++++++++++
 arm-1.6-03/arm/man/display.Rd |   15 ++++++++------
 8 files changed, 96 insertions(+), 40 deletions(-)

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Package tiff updated to version 0.1-4 with previous version 0.1-3 dated 2012-11-05

Title: Read and write TIFF images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between tiff versions 0.1-3 dated 2012-11-05 and 0.1-4 dated 2013-02-20

 DESCRIPTION |    7 ++++---
 MD5         |    6 +++---
 NEWS        |    4 ++++
 src/read.c  |    2 ++
 4 files changed, 13 insertions(+), 6 deletions(-)

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Package RSclient updated to version 0.7-1 with previous version 0.7-0 dated 2012-11-05

Title: Client for Rserve
Description: Client for Rserve, allowing to connect to Rserve instances and issue commands.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RSclient versions 0.7-0 dated 2012-11-05 and 0.7-1 dated 2013-02-20

 DESCRIPTION       |    7 +-
 MD5               |   16 +++---
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 src/qap.h         |    4 +
 10 files changed, 240 insertions(+), 47 deletions(-)

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Package PKI updated to version 0.1-1 with previous version 0.1-0 dated 2012-11-05

Title: Public Key Infrastucture for R based on the X.509 standard
Description: This package provides PKI functions such as verifyig certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between PKI versions 0.1-0 dated 2012-11-05 and 0.1-1 dated 2013-02-20

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 15 files changed, 310 insertions(+), 31 deletions(-)

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Package RCassandra updated to version 0.1-2 with previous version 0.1-1 dated 2012-11-05

Title: R/Cassandra interface
Description: This packages provides a direct interface (without the use of Java) to the most basic functionality of Apache Cassanda such as login, updates and queries.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RCassandra versions 0.1-1 dated 2012-11-05 and 0.1-2 dated 2013-02-20

 DESCRIPTION |    7 ++++---
 MD5         |    6 +++---
 NEWS        |    4 ++++
 src/cass.c  |    1 +
 4 files changed, 12 insertions(+), 6 deletions(-)

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New package mixOmics with initial version 4.1-3
Package: mixOmics
Type: Package
Title: Omics Data Integration Project
Version: 4.1-3
Date: 2012-12-11
Depends: R (>= 2.10), igraph0, rgl, lattice, pheatmap
Author: Sebastien Dejean, Ignacio Gonzalez, Kim-Anh Le Cao with contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet
Maintainer: Kim-Anh Le Cao
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.
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2013-02-20 07:40:24
Packaged: 2013-02-19 22:16:52 UTC; k.lecao
NeedsCompilation: no

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Package FisherEM updated to version 1.3.1 with previous version 1.3 dated 2013-02-13

Title: The Fisher-EM algorithm
Description: The FisherEM package provides an efficient algorithm for the unsupervised classification of high-dimensional data. This FisherEM algorithm models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Camille Brunet

Diff between FisherEM versions 1.3 dated 2013-02-13 and 1.3.1 dated 2013-02-20

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 8 files changed, 23 insertions(+), 32 deletions(-)

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