Mon, 05 Dec 2011

Package SBSA updated to version 0.1.2 with previous version 0.1.1 dated 2011-06-17

Title: Simplified Bayesian Sensitivity Analysis
Description: Simplified Bayesian Sensitivity Analysis
Author: Davor Cubranic and Paul Gustafson
Maintainer: Davor Cubranic

Diff between SBSA versions 0.1.1 dated 2011-06-17 and 0.1.2 dated 2011-12-05

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Package rJPSGCS updated to version 0.2-5 with previous version 0.2-4 dated 2011-10-09

Title: R-interface to gene drop Java Programs for Statistical Genetics and Computational Statistics (JPSGCS)
Description: R-interface to gene drop programs from Alun Thomas' Java Programs for Statistical Genetics and Computational Statistics (JPSGCS)
Author: Sigal Blay, Jinko Graham, Brad McNeney, Annick Nembot-Simo
Maintainer: Brad McNeney

Diff between rJPSGCS versions 0.2-4 dated 2011-10-09 and 0.2-5 dated 2011-12-05

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Package nleqslv updated to version 1.9.1 with previous version 1.9.0 dated 2011-09-16

Title: Solve systems of non linear equations
Description: Solve a system of non linear equations using a Broyden or a Newton method with a choice of global strategies such as linesearch and trust region. There are options for using a numerical or an analytical jacobian and fixed or automatic scaling of parameters.
Author: Berend Hasselman
Maintainer: Berend Hasselman

Diff between nleqslv versions 1.9.0 dated 2011-09-16 and 1.9.1 dated 2011-12-05

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Package obsSens updated to version 1.2 with previous version 1.1 dated 2011-02-05

Title: Sensitivity analysis for Observational studies.
Description: Observational studies are limited in that there could be an unmeasured variable related to both the response variable and the primary predictor. If this unmeasured variable were included in the analysis it would change the relationship (possibly changing the conclusions). Sensitivity analysis is a way to see how much of a relationship needs to exist with the unmeasured variable before the conclusions change. This package provides tools for doing a sensitivity analysis for regression (linear, logistic, and cox) style models.
Author: Greg Snow
Maintainer: Greg Snow

Diff between obsSens versions 1.1 dated 2011-02-05 and 1.2 dated 2011-12-05

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Package kinship2 updated to version 1.3.3 with previous version 1.3.1 dated 2011-10-12

Title: Pedigree functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria.
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Martha Matsumoto, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell

Diff between kinship2 versions 1.3.1 dated 2011-10-12 and 1.3.3 dated 2011-12-05

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Package highlight updated to version 0.3.1 with previous version 0.3.0 dated 2011-12-02

Title: Syntax highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom sweave driver performing syntax highlighting of R code chunks
Author: Romain Francois
Maintainer: Romain Francois

Diff between highlight versions 0.3.0 dated 2011-12-02 and 0.3.1 dated 2011-12-05

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Package HAC updated to version 0.1-8 with previous version 0.1-7 dated 2011-10-26

Title: Estimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, simulation methods and structural plots of high-dimensional Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin and Alexander Ristig
Maintainer: Ostap Okhrin

Diff between HAC versions 0.1-7 dated 2011-10-26 and 0.1-8 dated 2011-12-05

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Package gptk updated to version 1.05 with previous version 1.04 dated 2011-11-22

Title: Gaussian Processes Tool-Kit
Description: The gptk package implements a general-purpose toolkit for Gaussian process regression with a variety of covariance functions (e.g. RBF, Mattern, polynomial, etc). Based on a MATLAB implementation by Neil D. Lawrence. See inst/doc/index.html for more details.
Author: Alfredo A. Kalaitzis , Antti Honkela , Pei Gao , Neil D. Lawrence
Maintainer: Alfredo A. Kalaitzis

Diff between gptk versions 1.04 dated 2011-11-22 and 1.05 dated 2011-12-05

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Package genridge updated to version 0.6-0 with previous version 0.5-0 dated 2011-08-26

Title: Generalized ridge trace plots for ridge regression
Description: The genridge package introduces generalizations of the standard univariate ridge trace plot used in ridge regression and related methods. These graphical methods show both bias (actually, shrinkage) and precision, by plotting the covariance ellipsoids of the estimated coefficients, rather than just the estimates themselves. 2D and 3D plotting methods are provided, both in the space of the predictor variables and in the transformed space of the PCA/SVD of the predictors.
Author: Michael Friendly
Maintainer: Michael Friendly

Diff between genridge versions 0.5-0 dated 2011-08-26 and 0.6-0 dated 2011-12-05

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Package fastGHQuad updated to version 0.1-1 with previous version 0.1 dated 2011-12-03

Title: Fast Rcpp implementation of Gauss-Hermite quadrature
Description: Fast, numerically-stable Gauss-Hermite quadrature
Author: Alexander W Blocker
Maintainer: Alexander W Blocker

Diff between fastGHQuad versions 0.1 dated 2011-12-03 and 0.1-1 dated 2011-12-05

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Package emg updated to version 1.0.3 with previous version 1.0.2 dated 2011-10-25

Title: Exponentially Modified Gaussian (EMG) Distribution
Description: Provides basic distribution functions for a mixture model of a gaussian and exponential distribution.
Author: Shawn Garbett, Mark Kozdoba
Maintainer: Shawn Garbett

Diff between emg versions 1.0.2 dated 2011-10-25 and 1.0.3 dated 2011-12-05

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Package corrplot updated to version 0.60 with previous version 0.54 dated 2011-12-02

Title: Visualization of a correlation matrix
Description: The corrplot package is a graphical display of a correlation matrix, confidence interval. It also contains some algorithms to do matrix reordering.
Author: Taiyun Wei
Maintainer: Taiyun Wei

Diff between corrplot versions 0.54 dated 2011-12-02 and 0.60 dated 2011-12-05

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Package catR updated to version 2.1 with previous version 2.0 dated 2011-10-23

Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several starting rules, next item selection routines, stopping rules and ability estimators. Control methods for item exposure and content balancing are also included.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada)
Maintainer: David Magis

Diff between catR versions 2.0 dated 2011-10-23 and 2.1 dated 2011-12-05

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Package bnlearn updated to version 2.8 with previous version 2.7 dated 2011-10-08

Title: Bayesian network structure learning, parameter learning and inference
Description: Bayesian network structure learning (via constraint-based, score-based and hybrid algorithms), parameter learning (via ML and Bayesian estimators) and inference. This package implements the Grow-Shrink (GS) algorithm, the Incremental Association (IAMB) algorithm, the Interleaved-IAMB (Inter-IAMB) algorithm, the Fast-IAMB (Fast-IAMB) algorithm, the Max-Min Parents and Children (MMPC) algorithm, the ARACNE and Chow-Liu algorithms, the Hill-Climbing (HC) greedy search algorithm, the Tabu Search (TABU) algorithm, the Max-Min Hill-Climbing (MMHC) algorithm and the two-stage Restricted Maximization (RSMAX2) algorithm for both discrete and Gaussian networks, along with many score functions and conditional independence tests. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation and inference, conditional probability queries and cross-validation.
Author: Marco Scutari
Maintainer: Marco Scutari

Diff between bnlearn versions 2.7 dated 2011-10-08 and 2.8 dated 2011-12-05

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Package BiomarkeR updated to version 1.3 with previous version 1.2 dated 2011-06-17

Title: Paired (pBI) and Unpaired Biomarker Identifier (uBI) including a method to infer networks.
Description: This package allows to rank features and infer networks based on the Paired (pBI) and Unpaired Biomarker Identifier (uBI).
Author: Michael Netzer
Maintainer: Michael Netzer

Diff between BiomarkeR versions 1.2 dated 2011-06-17 and 1.3 dated 2011-12-05

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New package betafam with initial version 1.0
Package: betafam
Type: Package
Title: Detecting rare variants for quantitative traits using nuclear families
Version: 1.0
Date: 2011-12-01
Author: Wei Guo
Maintainer: Wei Guo
Depends: R (>= 2.4.0)
Description: To detecting rare variants for quantitative traits using nuclear families, the linear combination methods are proposed using the estimated regression coefficients from the multiple regression and regularized regression as the weights.
License: GPL (>= 2)
Packaged: 2011-12-05 18:54:26 UTC; weiguo
Repository: CRAN
Date/Publication: 2011-12-05 19:12:28

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Package RTextTools updated to version 1.3.2 with previous version 1.3.1 dated 2011-08-23

Title: Automatic Text Classification via Supervised Learning
Description: RTextTools is a machine learning package for automatic text classification that makes it simple for novice users to get started with machine learning, while allowing experienced users to easily experiment with different settings and algorithm combinations. The package includes nine algorithms for ensemble classification (svm, slda, boosting, bagging, random forests, glmnet, decision trees, neural networks, maximum entropy), comprehensive analytics, and thorough documentation.
Author: Timothy P. Jurka, Loren Collingwood, Amber E. Boydstun, Emiliano Grossman, Wouter van Atteveldt
Maintainer: Timothy P. Jurka

Diff between RTextTools versions 1.3.1 dated 2011-08-23 and 1.3.2 dated 2011-12-05

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Package RcppArmadillo updated to version 0.2.32 with previous version 0.2.31 dated 2011-11-29

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 2.4.0). 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 licenses under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates

Diff between RcppArmadillo versions 0.2.31 dated 2011-11-29 and 0.2.32 dated 2011-12-05

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Package PredictiveRegression updated to version 0.1-3 with previous version 0.1-2 dated 2011-11-20

Title: Prediction Intervals for Three Basic Statistical Models
Description: Three prediction algorithms described in the paper "On-line predictive linear regression" Annals of Statistics 37, 1566 - 1590 (2009)
Author: Vladimir Vovk and Ilia Nouretdinov
Maintainer: Vladimir Vovk

Diff between PredictiveRegression versions 0.1-2 dated 2011-11-20 and 0.1-3 dated 2011-12-05

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Package nga updated to version 1.4 with previous version 1.3 dated 2010-12-14

Title: NGA Earthquake Ground Motion Prediction Equations
Description: This package implements the earthquake ground motion prediction equations developed as part of the Next Generation Attenuation of Ground Motions (NGA) project coordinated by the Pacific Earthquake Engineering Research Center (PEER) in 2008. The models implemented in this package are AS08 (Abrahamson & Silva, 2008), BA08 (Boore & Atkinson, 2008), CB08 (Campbell & Bozorgnia, 2008), and CY08 (Chiou & Youngs, 2008). This numerical implementation has been validated by comparing the results for 128,000 test cases against the results obtained using the Fortran implementation composed by David M. Boore and Kenneth W. Campbell. Users are encouraged to view U.S. Geological Survey Open-File Report 1296, entitled "Implementation of the Next Generation Attenuation (NGA) Ground-Motion Prediction Equations in Fortran and R," by J. Kaklamanos, D. M. Boore, E. M. Thompson, and K. W. Campbell (2010) for further details on these programs. More details (including a change log) are available at .
Author: James Kaklamanos and Eric M. Thompson
Maintainer: James Kaklamanos

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Package maxent updated to version 1.3.0 with previous version 1.2.1 dated 2011-08-02

Title: Low-memory Multinomial Logistic Regression with Support for Text Classification
Description: maxent is an R package with tools for low-memory multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm package.
Author: Timothy P. Jurka
Maintainer: Timothy P. Jurka

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Package LaplacesDemon updated to version 11.12.05 with previous version 11.11.03 dated 2011-11-03

Title: Software for Bayesian Inference
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall

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Package goric updated to version 0.0-4 with previous version 0.0-3 dated 2011-11-21

Title: Generalized Order-Restricted Information Criterion
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate regression models
Author: Daniel Gerhard and Rebecca M. Kuiper
Maintainer: Rebecca M. Kuiper

Diff between goric versions 0.0-3 dated 2011-11-21 and 0.0-4 dated 2011-12-05

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Package DiceKriging updated to version 1.3.2 with previous version 1.3 dated 2011-08-18

Title: Kriging methods for computer experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville
Maintainer: Olivier Roustant

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Package zicounts (with last version 1.1.5) was removed from CRAN

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

2007-10-21 1.1.5
2005-01-28 1.1.4

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Package xlsReadWrite (with last version 1.3.2) was removed from CRAN

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

2007-04-15 1.3.2

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