Wed, 06 Jul 2011

Package sos updated to version 1.3-1 with previous version 1.3-0 dated 2010-06-23

Title: sos
Description: R related Search Engines
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Maintainer: Spencer Graves

Diff between sos versions 1.3-0 dated 2010-06-23 and 1.3-1 dated 2011-07-06

 DESCRIPTION           |    8 +++----
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 R/writeFindFn2xls.R   |    2 -
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 7 files changed, 41 insertions(+), 30 deletions(-)

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Package rvmbinary updated to version 0.1.2 with previous version 0.1 dated 2011-04-11

Title: RVM Binary Classification
Description: Performs binary classification of data using a Relevance Vector Machine
Author: Robert Lowe
Maintainer: Robert Lowe

Diff between rvmbinary versions 0.1 dated 2011-04-11 and 0.1.2 dated 2011-07-06

 DESCRIPTION            |    6 ++--
 R/gaus.R               |    4 +-
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 src/fullstatistics.cpp |   11 ++++---
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 src/main.cpp           |   24 +++++++++++-----
 11 files changed, 104 insertions(+), 46 deletions(-)

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New package rasterVis with initial version 0.10-2
Package: rasterVis
Type: Package
Title: Visualization methods for the raster package.
Version: 0.10-2
Date: 2011-07-04
Encoding: UTF-8
Author: Oscar Perpiñán Lamigueiro and Robert Hijmans
Maintainer: Oscar Perpiñán Lamigueiro
Description: The raster package defines classes and methods for spatial raster data access and manipulation. The rasterVis package complements raster providing a set of methods for enhanced visualization and interaction.
URL: http://rastervis.r-forge.r-project.org/
License: GPL-3
LazyLoad: yes
Depends: methods, raster(>= 1.8-34), RColorBrewer
Imports: grid, sp, lattice, latticeExtra, zoo, hexbin
Suggests: mgcv, rgl, ggplot2
Packaged: 2011-07-04 23:40:21 UTC; oscar
Repository: CRAN
Date/Publication: 2011-07-06 18:56:44

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New package orsk with initial version 0.1-1
Package: orsk
Type: Package
Title: Convertinging Odds Ratio to Relative Risk with Partial Data Information
Version: 0.1-1
Date: 2010-12-22
Author: Zhu Wang
Maintainer: Zhu Wang
Description: Convertinging Odds Ratio to Relative Risk with Partial Data Information
Depends: BB
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2011-07-05 23:04:17 UTC; Zwang
Repository: CRAN
Date/Publication: 2011-07-06 18:56:41

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Package mvabund updated to version 2.2-5.3 with previous version 2.2-4 dated 2011-06-30

Title: statistical methods for analysing multivariate abundance data
Description: A set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. See mvabund-package.Rd for details of overall package organization. The package is implemented with the Gnu Scientific Library (http://www.gnu.org/software/gsl/) and Rcpp (http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang

Diff between mvabund versions 2.2-4 dated 2011-06-30 and 2.2-5.3 dated 2011-07-06

 DESCRIPTION                       |   12 -
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 R/anova.manylm.R                  |  396 ++++++++++++++++----------------------
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 src/Makevars.win                  |    9 
 src/RtoAnovaCpp.cpp               |   51 ++--
 src/RtoGlm.cpp                    |   32 +--
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 29 files changed, 692 insertions(+), 730 deletions(-)

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Package mratios updated to version 1.3.16 with previous version 1.3.15 dated 2011-03-24

Title: Inferences for ratios of coefficients in the general linear model
Description: With this package, it is possible to perform (simultaneous) inferences for ratios of linear combinations of coefficients in the general linear model. In particular, tests and confidence interval estimations for ratios of treatment means in the normal one-way layout and confidence interval estimations like in (multiple) slope ratio and parallel line assays can be carried out. Moreover, it is possible to calculate the sample sizes required in comparisons with a control based on relative margins. For the simple two-sample problem, functions for a t-test for ratio-formatted hypotheses and the corresponding Fieller-type confidence interval are provided assuming homogeneous or heterogeneous group variances.
Author: Gemechis Dilba Djira, Mario Hasler, Daniel Gerhard, Frank Schaarschmidt
Maintainer: Frank Schaarschmidt

Diff between mratios versions 1.3.15 dated 2011-03-24 and 1.3.16 dated 2011-07-06

 DESCRIPTION        |    8 ++++----
 R/ratioVH.R        |   16 ++++++++--------
 R/simtest.ratioI.R |    6 +++---
 3 files changed, 15 insertions(+), 15 deletions(-)

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Package limitplot updated to version 1.2 with previous version 1.0 dated 2010-04-15

Title: Jitter/CI Plot with Ordered Points Below the Limit of Detection
Description: Values below a specified limit of detection are stacked in rows in order to reduce overplotting and create a clear graphical representation of your data.
Author: Omar E. Olmedo
Maintainer: Omar E. Olmedo

Diff between limitplot versions 1.0 dated 2010-04-15 and 1.2 dated 2011-07-06

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 8 files changed, 60 insertions(+), 153 deletions(-)

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Package grpreg updated to version 1.2-1 with previous version 1.2-0 dated 2011-06-22

Title: Regularization paths for regression models with grouped covariates
Description: Efficient algorithms for fitting the regularization path for linear or logistic regression models penalized by the group lasso, group bridge, or group MCP methods. The algorithm is based on the idea of a locally approximated coordinate descent.
Author: Patrick Breheny
Maintainer: Patrick Breheny

Diff between grpreg versions 1.2-0 dated 2011-06-22 and 1.2-1 dated 2011-07-06

 DESCRIPTION |   10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

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Package editrules updated to version 0.8 with previous version 0.7-1 dated 2011-06-29

Title: R package for parsing and manipulating edit rules
Description: Facilitates reading and manipulation of linear (in)equalities, converting them into matrix format (and vice versa) and checking if data are valid according to these rules. Sets of linear edits can be manipulated using Fourier-Motzkin elimination and variable substitution and solving error localization problems based on the generalized principle of Felligi and Holt.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge

Diff between editrules versions 0.7-1 dated 2011-06-29 and 0.8 dated 2011-07-06

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 editrules-0.8/editrules/R/errorLocalizer.R                     |   36 
 editrules-0.8/editrules/R/pkg.R                                |   34 
 editrules-0.8/editrules/R/reduce.R                             |   29 
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 43 files changed, 670 insertions(+), 548 deletions(-)

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Package caret updated to version 4.92 with previous version 4.91 dated 2011-06-09

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn

Diff between caret versions 4.91 dated 2011-06-09 and 4.92 dated 2011-07-06

 DESCRIPTION                 |   11 +-
 R/createGrid.R              |    1 
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 R/selectByFilter.R          |   35 ++++---
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 25 files changed, 467 insertions(+), 123 deletions(-)

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Package SixSigma updated to version 0.3.0 with previous version 0.2.1 dated 2011-04-01

Title: Six Sigma Tools for Quality and Process Improvement
Description: This package contains functions and utilities to perform Statistical Analysis for Six Sigma methodology. Through its outline DMAIC (Define, Measure, Analyze, Improve, Control), you can manage several Quality Management studies. The current version includes Capability Analysis, Gage R&R Study, Confidence Interval, Cause-and-effect diagram and Process Map. There will be new functions very soon for Capability Analysis, Control Charts, Reliability, OC Curves, Regression and Design of Experiments. See ?SixSigma for an Introduction.
Author: Emilio Lopez, Andres Redchuk, Javier M.Moguerza
Maintainer: Emilio Lopez

Diff between SixSigma versions 0.2.1 dated 2011-04-01 and 0.3.0 dated 2011-07-06

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 13 files changed, 19 insertions(+), 13 deletions(-)

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Package Rcpp updated to version 0.9.5 with previous version 0.9.4 dated 2011-04-12

Title: Seamless R and C++ Integration
Description: The Rcpp package provides a C++ library which facilitates 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. Several examples are included, and 753 unit tests in 338 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 this interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois

Diff between Rcpp versions 0.9.4 dated 2011-04-12 and 0.9.5 dated 2011-07-06

 ChangeLog                                             |   74 
 DESCRIPTION                                           |   10 
 R/00_classes.R                                        |    3 
 R/Module.R                                            |   16 
 R/loadRcppModules.R                                   |   10 
 R/populate.R                                          |   10 
 R/tools.R                                             |   13 
 R/zzz.R                                               |    3 
 cleanup                                               |    2 
 inst/NEWS                                             |   21 
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 42 files changed, 3252 insertions(+), 115 deletions(-)

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New package MultiPhen with initial version 0.1
Package: MultiPhen
Type: Package
Title: MultiPhen, a package for the genetic association testing of multiple phenotypes
Version: 0.1
Date: 2011-07-05
Author: Lachlan Coin, Paul O'reilly and Federico Calboli
Depends: MASS, abind, epitools, meta
Maintainer: Federico Calboli
Description: Genetic association analysis of for multiple genotypes and phenotypes
License: GPL
LazyLoad: yes
Packaged: 2011-07-05 13:06:10 UTC; greatsage
Repository: CRAN
Date/Publication: 2011-07-06 18:56:00

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Package JOP updated to version 2.0.3 with previous version 2.0.2 dated 2011-06-15

Title: Joint Optimization Plot
Description: JOP is a tool for simultanous optimization of multiple responses and visualization of the results. The visualization is done by the joint optimization plot introduced by Kuhnt and Erbruegge (2004).
Author: Sonja Kuhnt and Nikolaus Rudak
Maintainer: Nikolaus Rudak

Diff between JOP versions 2.0.2 dated 2011-06-15 and 2.0.3 dated 2011-07-06

 DESCRIPTION        |    8 ++++----
 R/locate.R         |   30 +++++++++++++++---------------
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 man/JOP-package.Rd |    4 ++--
 4 files changed, 30 insertions(+), 30 deletions(-)

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Package GPseq updated to version 0.5 with previous version 0.4 dated 2011-01-11

Title: gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
Description: Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.
Author: Sudeep Srivastava, Liang Chen
Maintainer: Sudeep Srivastava

Diff between GPseq versions 0.4 dated 2011-01-11 and 0.5 dated 2011-07-06

 DESCRIPTION  |    6 +++---
 R/wrapper2.R |    9 +++------
 2 files changed, 6 insertions(+), 9 deletions(-)

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Package BioMark updated to version 0.3.0 with previous version 0.2.6 dated 2011-02-08

Title: Find biomarkers in two-class discrimination problems
Description: The package implements PCLDA, PLSDA, and several t-tests to find those variables that allow for adequate discrimination between two classes. Apart from the usual approaches based on the size of model coefficients, a set of functions is provided that assess the stability of the potential biomarkers under crossvalidation.
Author: Ron Wehrens, Pietro Franceschi
Maintainer: Ron Wehrens

Diff between BioMark versions 0.2.6 dated 2011-02-08 and 0.3.0 dated 2011-07-06

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 22 files changed, 349 insertions(+), 258 deletions(-)

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