Mon, 07 Jul 2008

Package empiricalBayes updated to version 2.1 with previous version 2.0 dated 2008-05-07

Author: Zahra Montazeri , David R. Bickel
Bundle: empiricalBayes
Contains: HighProbability localFDR

Diff between empiricalBayes versions 2.0 dated 2008-05-07 and 2.1 dated 2008-07-07

 empiricalBayes-2.0/empiricalBayes/0402049v1.pdf                                   |only
 empiricalBayes-2.1/empiricalBayes/DESCRIPTION                                     |    9 +++++----
 empiricalBayes-2.1/empiricalBayes/HighProbability/DESCRIPTION.in                  |    4 +---
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 empiricalBayes-2.1/empiricalBayes/HighProbability/man/HighProbability2.Rd         |    3 +--
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 empiricalBayes-2.1/empiricalBayes/HighProbability/man/marginal.probability.Rd     |    3 +--
 empiricalBayes-2.1/empiricalBayes/localFDR/man/empirical1.Rd                      |    4 ++--
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 empiricalBayes-2.1/empiricalBayes/localFDR/man/localFDR1.Rd                       |    6 +++---
 empiricalBayes-2.1/empiricalBayes/localFDR/man/priorFDR.Rd                        |    6 +++---
 12 files changed, 24 insertions(+), 29 deletions(-)

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Package caTools updated to version 1.9 with previous version 1.8 dated 2007-10-09

Author: Jarek Tuszynski
Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off error free sum and cumsum, etc.

Diff between caTools versions 1.8 dated 2007-10-09 and 1.9 dated 2008-07-07

 CHANGES     |    7 +++++--
 DESCRIPTION |    8 ++++----
 R/zzz.R     |    6 +++---
 3 files changed, 12 insertions(+), 9 deletions(-)

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Package RJaCGH updated to version 1.5.4 with previous version 1.5.3 dated 2008-07-05

Author: Oscar Rueda and Ramon Diaz-Uriarte . zlib from Jean-loup Gailly and Mark Adler; see src/README. Function "getHostname.System" from package R.utils by Henrik Bengtsson.
Title: Reversible Jump MCMC for the analysis of CGH arrays.
Description: Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. The selection of the number of states is made via their posterior probability computed by Reversible Jump Markov Chain Monte Carlo Methods. Also returns probabilistic common regions for gains/losses.

Diff between RJaCGH versions 1.5.3 dated 2008-07-05 and 1.5.4 dated 2008-07-07

 Changes                             |    3 +
 DESCRIPTION                         |    6 +--
 R/RJaCGH.R                          |   30 +++++++++---------
 README.RJaCGH                       |    3 +
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 inst/doc/Implementing_pREC_in_C.pdf |binary
 src/nnhl.c                          |   58 ++++++++++++++++++------------------
 8 files changed, 57 insertions(+), 51 deletions(-)

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Package QRMlib updated to version 1.4.3 with previous version 1.4.2 dated 2007-11-17

Author: Alexander McNeil for S-Plus original; R port by Scott Ulman
Title: Provides R-language code to examine Quantitative Risk Management concepts
Description: This is a free R-language library designed to accompany the book Quantitative Risk Management: Concepts, Techniques and Tools by Alexander J. McNeil, Rudiger Frey and Paul Embrechts. A separate SPlus version can be downloaded from Alexander McNeil's URL at http://www.ma.hw.ac.uk/~mcneil/book/QRMlib.html

Diff between QRMlib versions 1.4.2 dated 2007-11-17 and 1.4.3 dated 2008-07-07

 DESCRIPTION                   |    8 
 R/functionsEVT.R              |   19 
 R/functionsUtility.R          |   62 
 inst/Chap8/S3-Statistics.R    |   18 
 inst/Docs/QRMlib.pdf          | 6006 ++++++++++++++++++++----------------------
 inst/README.txt               |   29 
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 man/1-BldQRMBookWorkspace.Rd  |   14 
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 src/gsl/gsl_math.h            |   43 
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 src/gsl/specfunc/gsl_sf_exp.h |   19 
 src/gsl/specfunc/gsl_sf_log.h |   22 
 14 files changed, 3225 insertions(+), 3105 deletions(-)

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New package Metabonomic with initial version 1.0
Package: Metabonomic
Type: Package
Title: GUI for Metabonomic Analysis
Version: 1.0
Date: 2008-07-07
Author: Jose L. Izquierdo
Maintainer: Jose L. Izquierdo
Description: Graphical User Interface for the Metabonomic Analysis (Baseline, Normalization, Peak Detection, PCA, PLS, Nearest Neigbourgt, Neural Network) developed to make easy this data analysis.
License: GPL version 2 or newer
Depends: tcltk, tcltk2, tkrplot, robustbase, mvoutlier, MASS, gpls, pls, splines, class, nnet, AMORE, neural, caMassClass, clusterSim, hddplot, scatterplot3d, relimp
Packaged: Mon Jul 7 18:31:53 2008; Jose

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Package robust updated to version 0.3-3 with previous version 0.3-2 dated 2008-07-05

Author: Jiahui Wang, Ruben Zamar , Alfio Marazzi , Victor Yohai , Matias Salibian-Barrera , Ricardo Maronna , Eric Zivot , David Rocke , Doug Martin , Kjell Konis .
Title: Insightful Robust Library
Description: A package of robust methods.

Diff between robust versions 0.3-2 dated 2008-07-05 and 0.3-3 dated 2008-07-07

 DESCRIPTION                                                   |   14 
 R/anova.glmRob.q                                              |    2 
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 R/anova.lmRob.q                                               |    3 
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 R/donostah.q                                                  |   52 
 R/fastcov.q                                                   |    5 
 R/glmRob.cubif.q                                              |    6 
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 R/glmRob.mallows.q                                            |    7 
 R/glmRob.q                                                    |    2 
 R/lmRob.effvy.q                                               |    3 
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 R/lmRob.q                                                     |    2 
 R/lmfmResQQPlot.q                                             |    4 
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 R/rb.q                                                        |    2 
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 man/donostah.Rd                                               |    8 
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 35 files changed, 1015 insertions(+), 544 deletions(-)

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Package rattle updated to version 2.3.46 with previous version 2.3.45 dated 2008-07-05

Author: Graham Williams
Title: A graphical user interface for data mining in R using GTK
Description: Rattle provides a Gnome (RGtk2) based interface to R functionality for data mining. The aim is to provide a simple and intuitive interface that allows a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, and build and evaluate models, and export models as PMML (predictive modelling markup language). All of this with knowing little about R. All R commands are logged and available for the user, as a tool to then begin interacting directly with R itself, if so desired. Rattle also exports a number of utility functions and the graphical user interface does not need to be run to deploy these.

Diff between rattle versions 2.3.45 dated 2008-07-05 and 2.3.46 dated 2008-07-07

 DESCRIPTION           |    6 +-
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 7 files changed, 187 insertions(+), 101 deletions(-)

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Package hwriter updated to version 0.92 with previous version 0.91 dated 2008-05-05

Author: Gregoire Pau
Title: HTML Writer - Outputs R objects in HTML format
Description: Easy-to-use and versatile functions to output R objects in HTML format

Diff between hwriter versions 0.91 dated 2008-05-05 and 0.92 dated 2008-07-07

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New package icomp with initial version 0.1
Package: icomp
Type: Package
Title: ICOMP criterion
Version: 0.1
Date: 2008-07-03
Author: Jake Ferguson
Maintainer: Jake Ferguson
Description: Calculates the ICOMP criterion and its variations
License: GPL (>= 2)
URL: http://taper-linux.msu.montana.edu/
Packaged: Mon Jul 7 14:45:08 2008; hornik

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New package fuzzyOP with initial version 1.0
Package: fuzzyOP
Type: Package
Title: Fuzzy numbers and the main mathematical operations
Version: 1.0
Date: 2008-06-15
Author: Aklan Semagul, Altindas Emine, Macit Rabiye, Umar Senay, Unal Hatice
Maintainer: Aklan Semagul, Altindas Emine, Macit Rabiye, Umar Senay, Unal Hatice
Description: This package contains functions which allow the depiction of fuzzy numbers. Besides, the main arithmetic operations are applied to fuzzy numbers and the extension principle for continuous functions can be applied and plotted.
License: GPL (>= 2)
Packaged: Mon Jul 7 14:51:40 2008; hornik

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Package fdrtool updated to version 1.2.5 with previous version 1.2.4 dated 2008-03-05

Author: Korbinian Strimmer.
Title: Estimation and Control of (Local) False Discovery Rates
Description: This package allows to estimate both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), and for the half-normal and correlation distributions.

Diff between fdrtool versions 1.2.4 dated 2008-03-05 and 1.2.5 dated 2008-07-07

 CHANGES                |   10 ++++++++++
 DESCRIPTION            |    8 ++++----
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 6 files changed, 32 insertions(+), 14 deletions(-)

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Package TSA updated to version 0.96 with previous version 0.94 dated 2008-02-12

Author: Kung-Sik Chan
Title: Time Series Analysis
Description: Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan

Diff between TSA versions 0.94 dated 2008-02-12 and 0.96 dated 2008-07-07

 DESCRIPTION        |    8 +--
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 15 files changed, 180 insertions(+), 181 deletions(-)

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Package LogConcDEAD updated to version 1.2-0 with previous version 1.1-2 dated 2008-06-19

Author: Madeleine Cule, Robert Gramacy, Richard Samworth
Title: Maximum likelihood estimation of a log-concave density
Description: Computes the maximum likelihood estimator from an i.i.d. sample of data from a log-concave density in any number of dimensions. Plots are available for 1- and 2-d data.

Diff between LogConcDEAD versions 1.1-2 dated 2008-06-19 and 1.2-0 dated 2008-07-07

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 20 files changed, 203 insertions(+), 261 deletions(-)

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New package CADStat with initial version 2.1-06
Package: CADStat
Version: 2.1-06
Date: 2008-07-06
Title: Provides a GUI to several statistical methods for biological inferences
Author: Lester Yuan, Tom Stockton, Doug Bronson, Pasha Minallah, and Mark Fitzgerald
Maintainer: Lester Yuan
Depends: JGR, XML, lattice, bio.infer, gdata, gmodels, car, MASS, quantreg, rpart
Description: Using JGR, provides a GUI to several statistical methods - scatterplot, boxplot, linear regression, generalized linear regression, quantile, regression, conditional probability calculations, and regression trees.
License: GPL Version 2 or newer
URL: http://www.rforge.net/CADStat/
Packaged: Sun Jul 6 21:38:23 2008; Lester

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New package HAPim with initial version 1.0
Package: HAPim
Type: Package
Title: HapIM
Version: 1.0
Date: 2008-07-01
Author: S.Dejean, N.Oumouhou, D.Estivals, B.Mangin
Maintainer: Brigitte Mangin
Description: The package provides a set of functions whose aim is to propose 4 methods of QTL detection and fine mapping.HAPIM LD is an interval-mapping method designed for unrelated individuals with no family information and is based on a maximum-likelihood calculation.HAPIM LDL is an interval-mapping method which uses family information of individuals and combines linkage and linkage disequilibrium.It is based on a maximum-likelihood calculation.HAPLOMAX gives an analysis of variance with a sire effect and a haplotype effect. HAPLOMAX HS gives an analysis of variance with a sire effect and a haplotype effect in half-sire design.
License: GPL
Packaged: Mon Jul 7 09:15:08 2008; sdejean

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