Sat, 23 Jul 2011

Package clime updated to version 0.3 with previous version 0.2 dated 2011-02-03

Title: Constrained L1-minimization for Inverse (covariance) Matrix Estimation
Description: A robust constrained L1 minimization method for estimating a large sparse inverse covariance matrix (aka precision matrix), and recovering its support for building graphical models. The computation uses linear programming.
Author: T. Tony Cai, Weidong Liu and Xi (Rossi) Luo
Maintainer: Xi (Rossi) Luo

Diff between clime versions 0.2 dated 2011-02-03 and 0.3 dated 2011-07-23

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 DESCRIPTION    |    8 ++++----
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 4 files changed, 8 insertions(+), 6 deletions(-)

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New package rtfbs with initial version 0.1.0
Copyright: The code in src/pcre is Copyright (c) 1997-2010 University of Cambridge. All other code is Copyright (c) 2002-2011 University of California, Cornell University.
Package: rtfbs
Maintainer: RTFBS Group
License: BSD
Title: R Transcription Factor Binding Site identification tool
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Description: RTFBS identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by GC content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R.
Version: 0.1.0
URL: http://compgen.bscb.cornell.edu/rtfbs
Date: 2011-07-18
Depends: stats, rphast
Collate: 'tfbs.R'
Packaged: 2011-07-23 18:16:11 UTC; melissa
Repository: CRAN
Date/Publication: 2011-07-23 20:15:40

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Package caroline updated to version 0.5.4 with previous version 0.5.1 dated 2011-06-07

Title: A Collection of General Purpose Functions for R
Description: Great utilities that you won't be able to live without.
Author: David M. Schruth
Maintainer: David M. Schruth

Diff between caroline versions 0.5.1 dated 2011-06-07 and 0.5.4 dated 2011-07-23

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Package RgoogleMaps updated to version 1.1.9.11 with previous version 1.1.9.8 dated 2011-06-29

Title: Overlays on Google map tiles in R
Description: This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling. NOTE: To do anything but downloading static map tiles, RgoogleMaps needs EITHER png OR ReadImages OR rimage installed ! png (default) is your package if you prefer png file format and ReadImages or rimage if you prefer jpg format. In the latter cases, you will also need the libjpeg library installed.
Author: Markus Loecher, Sense Networks
Maintainer: "Markus Loecher, Sense Networks"

Diff between RgoogleMaps versions 1.1.9.8 dated 2011-06-29 and 1.1.9.11 dated 2011-07-23

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Package pensim updated to version 1.1.3 with previous version 1.0.3 dated 2011-06-30

Title: Simulation of high-dimensional data and parallelized repeated penalized regression
Description: Simulation of continuous, correlated high-dimensional data with time to event or binary response, and parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with repeated starts and two-dimensional tuning of the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C. Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron

Diff between pensim versions 1.0.3 dated 2011-06-30 and 1.1.3 dated 2011-07-23

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New package HAC with initial version 0.1-0
Package: HAC
Type: Package
Title: Estimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC)
Version: 0.1-0
Date: 2011-04-20
Author: Ostap Okhrin and Alexander Ristig
Maintainer: Ostap Okhrin
Lazyload: yes
Depends: R (>= 2.9.1), copula
Imports: fBasics
Description: The estimation of the structure, simulation methods and structural plots of Hierarchical Archimedean Copulae (HAC) are the major applications which are covered by this package. In combination with this package the class "hac" is implemented. Estimation methods for empirical copulae are also included. There is, however, still room for improvement: 1. Probability density functions are only available up to the third dimension. 2. Although the copula models which are estimated or constructed provide a wide range of models, some complex models have to be approximated.
License: GPL (>= 3)
URL: http://lehre.wiwi.hu-berlin.de/Professuren/quantitativ/statistik/members/personalpages/o2
Packaged: 2011-07-23 16:36:31 UTC; Alex
Repository: CRAN
Date/Publication: 2011-07-23 17:15:56

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Package rcdklibs updated to version 1.4.1 with previous version 1.3.11 dated 2011-06-19

Title: rcdklib - CDK libraries packaged for R
Description: This package provides the CDK libraries for use in the R environment. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the rcdk package. Note that it is possible to directly interact with the CDK using rJava. However rcdk exposes functionality in a more idiomatic way
Author: Rajarshi Guha
Maintainer: Rajarshi Guha

Diff between rcdklibs versions 1.3.11 dated 2011-06-19 and 1.4.1 dated 2011-07-23

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Package rcdk updated to version 3.1.2 with previous version 3.1.1 dated 2011-06-19

Title: rcdk - Interface to the CDK Libraries
Description: This package allows the user to access functionality in the CDK, a Java framework for cheminformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition the CDK API allows the user to view structures in 2D.
Author: Rajarshi Guha
Maintainer: Rajarshi Guha

Diff between rcdk versions 3.1.1 dated 2011-06-19 and 3.1.2 dated 2011-07-23

 CHANGELOG          |    4 ++++
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Package nlme updated to version 3.1-102 with previous version 3.1-101 dated 2011-05-06

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro (S version), Douglas Bates (up to 2007), Saikat DebRoy (up to 2002), Deepayan Sarkar (up to 2005), the R Core team.
Maintainer: R-core

Diff between nlme versions 3.1-101 dated 2011-05-06 and 3.1-102 dated 2011-07-23

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Package foreign updated to version 0.8-45 with previous version 0.8-44 dated 2011-04-13

Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...
Description: Functions for reading and writing data stored by statistical packages such as Minitab, S, SAS, SPSS, Stata, Systat, ..., and for reading and writing dBase files.
Author: R-core members, Saikat DebRoy , Roger Bivand and others: see COPYRIGHTS file in the sources.
Maintainer: R-core

Diff between foreign versions 0.8-44 dated 2011-04-13 and 0.8-45 dated 2011-07-23

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New package Tinflex with initial version 0.1
Package: Tinflex
Type: Package
Title: Tinflex - Universal non-uniform random number generator
Version: 0.1
Date: 2011-07-07
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold
Suggests: Runuran, rvgtest
Description: A universal non-uniform random number generator for quite arbitrary distributions with piecewise twice differentiable densities.
License: GPL (>= 2)
Packaged: 2011-07-08 06:44:38 UTC; leydold
Repository: CRAN
Date/Publication: 2011-07-23 16:15:10

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Package RghcnV3 updated to version 1.5 with previous version 1.1 dated 2011-06-28

Title: Global Historical Climate Network Version 3
Description: The Rghcn package provides the core functions required to download and format the GHCN V3 data and process it into temperature series and temperature anomaly series. The data is reformated so that integration with objects in the system is straightforward. In addition, there are core functions required to download and create land masks and functions to download and import Sea Surface Temperature (SST) data.
Author: Steven Mosher
Maintainer: Steven Mosher

Diff between RghcnV3 versions 1.1 dated 2011-06-28 and 1.5 dated 2011-07-23

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Package MASS updated to version 7.3-14 with previous version 7.3-13 dated 2011-04-13

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).
Author: S original by Venables & Ripley. R port by Brian Ripley, following partial ports by Kurt Hornik and Albrecht Gebhardt around 1998.
Maintainer: Brian Ripley

Diff between MASS versions 7.3-13 dated 2011-04-13 and 7.3-14 dated 2011-07-23

 DESCRIPTION                      |   11 +++++------
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 R/lda.R                          |    3 ++-
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New package xgrid with initial version 0.1-11
Package: xgrid
Type: Package
Title: Access Apple Xgrid using R
Version: 0.1-11
Date: 2011-07-19
Depends:
Suggests:
Author: Nicholas Horton
Maintainer: Nicholas Horton
Description: Functions to distribute and collate results from simulation studies and other computationally expensive tasks to Apple Xgrid clusters from within R
License: GPL
LazyLoad: yes
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: mosaic
Repository/R-Forge/Revision: 527
Date/Publication: 2011-07-23 14:44:28
Packaged: 2011-07-19 21:21:12 UTC; rforge

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New package wordcloud with initial version 1.1
Package: wordcloud
Type: Package
Title: Word Clouds
Version: 1.1
Date: 2011-06-06
Author: Ian Fellows
Maintainer: Ian Fellows
Description: Pretty word clouds
License: LGPL-2.1
LazyLoad: yes
Depends: methods, Rcpp (>= 0.9.4)
Suggests: tm, RColorBrewer
LinkingTo: Rcpp
Packaged: 2011-07-15 15:03:13 UTC; ianfellows
Repository: CRAN
Date/Publication: 2011-07-23 14:44:26

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Package wnominate updated to version 0.96 with previous version 0.95 dated 2011-05-26

Title: WNOMINATE Roll Call Analysis Software.
Description: Estimates Poole and Rosenthal W-NOMINATE scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
Author: Keith Poole , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: Jeffrey Lewis

Diff between wnominate versions 0.95 dated 2011-05-26 and 0.96 dated 2011-07-23

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Package visualizationTools updated to version 0.2.02 with previous version 0.2.01 dated 2011-05-23

Title: Package contains a few functions to visualize statistical circumstances.
Description: Package contains function to visualize a t-test, the power of a t-test, control charts and the influence of regulating them, Oc-curves, the Law of large Numbers and confidence intervals.
Author: Thomas Roth Etienne Stockhausen
Maintainer: T. Roth E. Stockhausen

Diff between visualizationTools versions 0.2.01 dated 2011-05-23 and 0.2.02 dated 2011-07-23

 DESCRIPTION                       |    8 ++++----
 R/plot.power.htest.R              |    4 ++--
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New package support.CEs with initial version 0.2-0
Package: support.CEs
Type: Package
Title: Basic functions for supporting an implementation of choice experiments
Version: 0.2-0
Date: 2011-07-14
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
Description: The support.CEs package provides seven basic functions that support an implementation of choice experiments.
License: GPL (>= 2)
Depends: DoE.base, MASS, simex, survival
Repository: CRAN
LazyLoad: yes
LazyData: yes
Packaged: 2011-07-14 05:13:43 UTC; user
Date/Publication: 2011-07-23 14:43:11

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New package stratasphere with initial version 1.0
Package: stratasphere
Type: Package
Title: Stratified Spherical Approximate Conditional Modeling
Version: 1.0
Date: 2011-07-07
Author: Daniel Percival
Maintainer: Daniel Percival
Description: For data where the observations occur or are collected in a stratified fashion, the strata level effect is sometimes not of interest or is simply impossible to estimate. Conditioning on the strata eliminates these difficulties, but leads to a combinatorially complex calculation. The spherical approximate method replaces this complex calculation with a closed form solution, leading to a simple fixed point iteration method for fitting the linear model. This package implements linear model fitting via Stratasphere(), and stepwise regression and boosting extensions via StratasphereStep() and StratasphereBoost(), respectively. Note that this package is distributed under the Apache 2.0 license.
License: Apache License 2.0
Depends: survival, mboost, hash
LazyLoad: yes
Packaged: 2011-07-23 14:47:37 UTC; dancsi
Repository: CRAN
Date/Publication: 2011-07-23 15:14:07

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Package sqldf updated to version 0.4-1.2 with previous version 0.4-1 dated 2011-06-29

Title: Perform SQL Selects on R Data Frames
Description: Manipulate R data frames using SQL.
Author: G. Grothendieck
Maintainer: G. Grothendieck

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Package stashR updated to version 0.3-4 with previous version 0.3-3 dated 2009-03-27

Title: A Set of Tools for Administering SHared Repositories
Description: A Set of Tools for Administering SHared Repositories
Author: Sandy Eckel, Roger D. Peng
Maintainer: Roger D. Peng

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Package sparkTable updated to version 0.9.1 with previous version 0.1.3 dated 2010-09-13

Title: Sparklines and graphical tables for tex and html
Description: Create Sparklines and graphical tables for documents and websites
Author: Alexander Kowarik, Bernhard Meindl, Stefan Zechner
Maintainer: Alexander Kowarik , Bernhard Meindl , Stefan Zechner

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Package spacetime updated to version 0.5-1 with previous version 0.5-0 dated 2011-07-02

Title: classes and methods for spatio-temporal data
Description: A package with classes and methods for spatio-temporal data. In particular, space-time regular lattices, sparse lattices, and irregular data are supported, but no topologies with S/T interactions sucha s space-time prisms. Utility functions are provided, e.g. for plotting data as map sequences or multiple time series; for spatial and temporal selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma, with contributions by Benedict Graeler and Tom Gottfried
Maintainer: Edzer Pebesma

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Package sp updated to version 0.9-84 with previous version 0.9-83 dated 2011-06-15

Title: classes and methods for spatial data
Description: A package that provides classes and methods for spatial data. The classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma , Roger Bivand and others
Maintainer: Edzer Pebesma

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Package sn updated to version 0.4-17 with previous version 0.4-16 dated 2010-08-30

Title: The skew-normal and skew-t distributions
Description: Functions for manipulating skew-normal and skew-t probability distributions, and for fitting them to data, in the scalar and in the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

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Package smatr updated to version 3.2.2 with previous version 3.2.0 dated 2011-04-27

Title: (Standardised) Major Axis Estimation and Testing Routines
Description: This package provides methods of fitting bivariate lines in allometry using the major axis (MA) or standardised major axis (SMA), and for making inferences about such lines. The available methods of inference include confidence intervals and one-sample tests for slope and elevation, testing for a common slope or elevation amongst several allometric lines, constructing a confidence interval for a common slope or elevation, and testing for no shift along a common axis, amongst several samples.
Author: David Warton , Remko Duursma, Daniel Falster and Sara Taskinen.
Maintainer: David Warton

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Package simFrame updated to version 0.4.2 with previous version 0.4.1 dated 2011-03-21

Title: Simulation framework
Description: A general framework for statistical simulation.
Author: Andreas Alfons
Maintainer: Andreas Alfons

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Package siar updated to version 4.1.1 with previous version 4.1 dated 2011-03-31

Title: Stable Isotope Analysis in R
Description: This package takes data on organism isotopes and fits a Bayesian model to their dietary habits based upon a Gaussian likelihood with a mixture dirichlet-distributed prior on the mean. See siardemo() for an example. The latest version includes SiBER metrics. Version 4.1.1 contains a bug fix to the function standard.ellipse
Author: Andrew Parnell and Andrew Jackson
Maintainer: Andrew Parnell

Diff between siar versions 4.1 dated 2011-03-31 and 4.1.1 dated 2011-07-23

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New package s4vd with initial version 1.0
Package: s4vd
Version: 1.0
Title: Biclustering via sparse singular value decomposition incorporating stability selection
Date: 2010-07-27
Author: Martin Sill, Sebastian Kaiser
Maintainer: Martin Sill
Depends: biclust,methods
Suggests: isa2
Description: The main function s4vd performs a biclustering via sparse singular value decomposition with a nested stability selection. The results is an biclust object and thus all methods of the biclust package can be applied.
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: s4vd
Repository/R-Forge/Revision: 89
Date/Publication: 2011-07-23 14:42:30
Packaged: 2011-07-07 21:23:00 UTC; rforge

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New package rsae with initial version 0.1-2
Package: rsae
Type: Package
Title: Robust Small Area Estimation
Version: 0.1-2
Date: 2011-07-06
Author: Tobias Schoch
Maintainer: Tobias Schoch
Description: Robust Small Area Estimation. Robust Basic Unit- and Area-Level Models
Suggests: robustbase, nlme
License: GPL (>= 2) | FreeBSD
LazyLoad: yes
Packaged: 2011-07-11 19:37:29 UTC; tobias
Repository: CRAN
Date/Publication: 2011-07-23 14:42:27

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New package roxygen2 with initial version 2.0
Package: roxygen2
Version: 2.0
License: GPL (>= 2)
Description: A Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE.
Title: In-source documentation for R
Author: Hadley Wickham , Peter Danenberg , Manuel Eugster
Maintainer: Hadley Wickham
Imports: stringr (>= 0.5), tools, brew
Suggests: testthat
Depends: digest
Collate: 'cache.R' 'description.R' 'parse.R' 'parse-preref.R' 'parse-srcref.R' 'parse-registry.R' 'rd-file-api.R' 'rd-tag-api.R' 'roclet-collate.R' 'roclet-namespace.R' 'roclet-rd.R' 'roclet.R' 'roxygen.R' 'roxygenize.R' 'topo-sort.R' 'utils.R' 'template.R' 'rd-parse.R'
Packaged: 2011-07-14 17:01:58 UTC; hadley
Repository: CRAN
Date/Publication: 2011-07-23 14:42:24

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Package refund updated to version 0.1-4 with previous version 0.1-3 dated 2011-05-15

Title: Regression with Functional Data
Description: Functions for regression with functional data. The principal methods currently implemented are (I) regression of scalar responses on functional predictors, by (longitudinal) penalized functional regression and functional principal component regression; and (II) regression of functional responses on scalar predictors, by penalized OLS or GLS.
Author: Coordinating authors: Ciprian Crainiceanu and Philip Reiss . Contributors: Jeff Goldsmith and Lei Huang
Maintainer: Lei Huang

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New package rje with initial version 1.0
Package: rje
Type: Package
Title: Miscellaneous useful functions
Version: 1.0
Date: 2011-07-14
Author: Robin Evans
Maintainer: Robin Evans
Description: A series of useful functions, some of which are available in other forms in other packages, but many of which have been extended in some way.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2011-07-14 22:33:14 UTC; rje42
Repository: CRAN
Date/Publication: 2011-07-23 14:42:22

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Package rdyncall updated to version 0.7.3 with previous version 0.7.2 dated 2011-04-27

Title: Improved Foreign Function Interface (FFI) and Dynamic Bindings to C Libraries (e.g. OpenGL)
Description: The package provides a cross-platform framework for dynamic binding of C libraries using a flexible Foreign Function Interface (FFI). The FFI supports almost all fundamental C types, multiple calling conventions, symbolic access to foreign C struct/union data types and wrapping of R functions as C callback function pointers. Dynamic bindings to shared C libraries are data-driven by cross-platform binding specification using a compact plain text format ; an initial repository of bindings to a couple of common C libraries (OpenGL, SDL, Expat, glew, CUDA, OpenCL, ODE, R) comes with the package. The package includes a variety of technology demos and OS-specific notes for installation of shared libraries.
Author: Daniel Adler
Maintainer: Daniel Adler

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Permanent link

Package rattle updated to version 2.6.7 with previous version 2.6.6 dated 2011-04-10

Title: Graphical user interface for data mining in R
Description: Rattle (the R Analytic Tool To Learn Easily) 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, build and evaluate models, and export models as PMML (predictive modelling markup language) or as scores. All of this with knowing little about R. All R commands are logged and commented through the log tab. Thus they are available to the user as a script file or as an aide for the user to learn R or to copy-and-paste directly into R itself. Rattle also exports a number of utility functions and the graphical user interface, invoked as rattle(), does not need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams

Diff between rattle versions 2.6.6 dated 2011-04-10 and 2.6.7 dated 2011-07-23

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More information about rattle at CRAN
Permanent link

Package rasterVis updated to version 0.10-3 with previous version 0.10-2 dated 2011-07-06

Title: Visualization methods for the raster package
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.
Author: Oscar Perpiñán Lamigueiro and Robert Hijmans
Maintainer: Oscar Perpiñán Lamigueiro

Diff between rasterVis versions 0.10-2 dated 2011-07-06 and 0.10-3 dated 2011-07-23

 DESCRIPTION                |   16 ++++++++--------
 NAMESPACE                  |    6 ++++--
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More information about rasterVis at CRAN
Permanent link

Package raster updated to version 1.9-1 with previous version 1.8-39 dated 2011-07-05

Title: Geographic analysis and modeling with raster data
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions, as well as map algebra. Processing of very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans

Diff between raster versions 1.8-39 dated 2011-07-05 and 1.9-1 dated 2011-07-23

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More information about raster at CRAN
Permanent link

New package pxR with initial version 0.20
Package: pxR
Type: Package
Title: PC-Axis with R
Version: 0.20
Date: 2011-07-11
Encoding: UTF-8
Author: Francisco J. Viciana, Carlos J. Gil Bellosta, Oscar Perpiñán Lamigueiro, Vicente David Canto Casasola, Jorge Iván Vélez.
Author@R: c(person("Francisco J.", "Viciana", email= "franciscoj.viciana@juntadeandalucia.es", role='aut'), person("Carlos J.", "Gil Bellosta", email="cgb@datanalytics.com", role='aut'), person("Oscar", "Perpiñán Lamigueiro", email="oscar.perpinan@upm.es", role=c('cre', 'aut')), person("Vicente David", "Canto Casasola", email= "vicented.canto.sspa@juntadeandalucia.es", role='aut'), person("Jorge Iván", "Vélez", email="jorgeivanvelez@gmail.com", role='aut') )
Maintainer: Oscar Perpiñán Lamigueiro
Description: The pxR package provides a set of functions for reading and writing PC-Axis files, used by different statistical organizations around the globe for data disemination.
URL: http://pxr.r-forge.r-project.org/
License: GPL-3
LazyLoad: yes
LazyData: yes
Packaged: 2011-07-23 15:04:22 UTC; oscar
Repository: CRAN
Date/Publication: 2011-07-23 15:55:28

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Permanent link

Package gstat updated to version 1.0-0 with previous version 0.9-82 dated 2011-06-27

Title: spatial and spatio-temporal geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma and others
Maintainer: Edzer Pebesma

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Package devtools updated to version 0.4 with previous version 0.3 dated 2011-06-30

Title: Tools to make developing R code easier
Description: Collection of package development tools
Author: Hadley Wickham
Maintainer: Hadley Wickham

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Package R2jags updated to version 0.02-16 with previous version 0.02-15 dated 2011-03-30

Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Author: Yu-Sung Su , Masanao Yajima ,
Maintainer: Yu-Sung Su

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Package qualityTools updated to version 1.45 with previous version 1.44 dated 2011-06-01

Title: Statistical Methods for Quality Science
Description: This is a package for teaching statistical methods in the field of Quality Science. It covers distribution fitting, process capability, Gage R&R, factorial, fractional factorial design as well as response surface methods including the use of desirability functions. Define - Pareto Chart; Measure - Probability and Quantile-Quantile Plots, Process Capability Ratios for various distributions and Gage RR Analyze i.e. Pareto Chart, Multi-Vari Chart, Dot Plot; Improve - Full and fractional factorial, response surface and mixture designs as well as the desirability approach for simultaneous optimization of more than one response variable. Normal, Pareto and Lenth Plot of effects as well as Interaction Plots; Control - Quality Control Charts can be found in the qcc package. The focus is on teaching the statistical methodology used in the Quality Sciences.
Author: Thomas Roth
Maintainer: Thomas Roth

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Package profdpm updated to version 3.0 with previous version 2.0 dated 2010-05-25

Title: Profile Dirichlet Process Mixtures
Description: This package facilitates profile inference (inference at the posterior mode) for a class of product partition models (PPM). The Dirichlet process mixture is currently the only available member of this class. These methods search for the maximum posterior (MAP) estimate for the data partition in a PPM.
Author: Matt Shotwell
Maintainer: Matt Shotwell

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Package pracma updated to version 0.7-3 with previous version 0.6-3 dated 2011-06-29

Title: Practical Numerical Math Functions
Description: This package provides R implementations of functions in numerical analysis, with a special view on on optimization and time series routines. Uses Matlab/Octave function names where appropriate to simplify porting.
Author: Hans W Borchers
Maintainer: HwB

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New package productplots with initial version 0.1
Package: productplots
Type: Package
Title:
Version: 0.1
Author: Hadley Wickham
Maintainer: Hadley Wickham
Depends: ggplot2, plyr
Suggests: reshape2, testthat
License: GPL-2
LazyData: true
Description:
Collate: 'calculate.r' 'divide.r' 'labels.r' 'margin.r' 'parse.r' 'partition-1d.r' 'partition-2d.r' 'partition-tile.r' 'partition.r' 'plot.r' 'productplots.r' 'templates.r' 'utils.r'
Packaged: 2011-07-13 21:26:34 UTC; hadley
Repository: CRAN
Date/Publication: 2011-07-23 14:41:29

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New package prLogistic with initial version 1.0
Package: prLogistic
Type: Package
Version: 1.0
Date: 2011-07-13
Title: Estimation of Prevalence Ratios using Logistic Models
Author: Raydonal Ospina and Leila D. Amorim .
Maintainer: Raydonal Ospina
Depends: R (>= 2.10.0), boot, methods, stats, stats4, lme4, Hmisc
Description: Estimation of prevalence ratios using logistic models and confidence intervals with delta and bootstrap methods.
License: GPL-2
LazyLoad: yes
LazyData: yes
Packaged: 2011-07-13 17:11:10 UTC; raydonal
Repository: CRAN
Date/Publication: 2011-07-23 14:41:07

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Package popbio updated to version 2.3.1 with previous version 2.2 dated 2011-03-23

Title: Construction and analysis of matrix population models
Description: Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Author: Chris Stubben, Brook Milligan, Patrick Nantel
Maintainer: Chris Stubben

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New package playitbyr with initial version 0.1-1
Package: playitbyr
Type: Package
Title: Representing and exploring data through sound
Version: 0.1-1
Date: 2011-07-12
Author: Ethan Brown
Maintainer: Ethan Brown
Depends: R (>= 2.12.0), audio
Description: playitbyr is a flexible toolkit for data analysis and exploration in R. The functions allow the user to map data onto sonic parameters like pitch, tempo, and rhythm, and output sound and sound files.
URL: http://playitbyr.r-forge.r-project.org/
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2011-07-15 04:03:22 UTC; fortis
Repository: CRAN
Date/Publication: 2011-07-23 14:40:57

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Package phylotools updated to version 0.1.1 with previous version 0.0.7.4 dated 2010-11-03

Title: Phylogenetic tools for Eco-phylogenetics
Description: Building supermatrix for DNA barcodes using different genes, calculating the inequality among lineages and phylogenetic similarity for very large dataset using slicing methods by invoking Phylocom.
Author: Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Maintainer: Jinlong Zhang

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Package pegas updated to version 0.4 with previous version 0.3-4 dated 2011-04-01

Title: Population and Evolutionary Genetics Analysis System
Description: pegas provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences including coalescence analyses.
Author: Emmanuel Paradis, Alastair Potts
Maintainer: Emmanuel Paradis

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Package oce updated to version 0.4-1 with previous version 0.3-1 dated 2011-06-22

Title: Analysis of Oceanographic data
Description: Supports the analysis of Oceanographic data, including ADP measurements, CTD measurements, sectional data, sea-level time series, coastline files, etc. Provides functions for calculating seawater properties such as potential temperature and density, as well as derived properties such as buoyancy frequency and dynamic height.
Author: Dan Kelley
Maintainer: Dan Kelley

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 oce-0.4-1/oce/inst/extdata/ctd.cnv         |  388 ++++++++++++++++-------------
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Package nlts updated to version 0.1-8 with previous version 0.1-7 dated 2010-09-27

Title: (non)linear time series analysis
Description: R functions for (non)linear time series analysis. A core topic is order estimation through cross-validation.
Author: Ottar N. Bjornstad
Maintainer: Ottar N. Bjornstad

Diff between nlts versions 0.1-7 dated 2010-09-27 and 0.1-8 dated 2011-07-23

 CHANGES                 |    3 ++
 DESCRIPTION             |    8 ++---
 NAMESPACE               |    1 
 R/nlts.R                |   65 ++++++++++++++++++++++++++++++++++++++++++++++--
 man/predict.ll.order.Rd |only
 5 files changed, 71 insertions(+), 6 deletions(-)

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Package network updated to version 1.7 with previous version 1.6 dated 2011-01-29

Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts , David Hunter , and Mark S. Handcock
Maintainer: Carter T. Butts

Diff between network versions 1.6 dated 2011-01-29 and 1.7 dated 2011-07-23

 ChangeLog                |   23 +++++++++++++++++++++++
 DESCRIPTION              |   10 +++++-----
 R/coercion.R             |   20 +++++++++++++++-----
 R/constructors.R         |   19 +++++++++----------
 R/printsum.R             |   46 +++++++++++++++++++++++++++-------------------
 data/emon.RData          |binary
 data/flo.RData           |binary
 man/as.matrix.network.Rd |   10 ++++++----
 man/network-operators.Rd |    2 +-
 9 files changed, 86 insertions(+), 44 deletions(-)

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Package RcppArmadillo updated to version 0.2.27 with previous version 0.2.26 dated 2011-07-23

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 2.1.91). 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 0.2.26 dated 2011-07-23 and 0.2.27 dated 2011-07-23

 ChangeLog                                            |    6 
 DESCRIPTION                                          |   10 
 inst/NEWS                                            |   11 
 inst/include/armadillo_bits/Col_bones.hpp            |    6 
 inst/include/armadillo_bits/Col_meat.hpp             |   72 ++
 inst/include/armadillo_bits/Mat_bones.hpp            |    7 
 inst/include/armadillo_bits/Mat_meat.hpp             |   34 +
 inst/include/armadillo_bits/Row_bones.hpp            |    6 
 inst/include/armadillo_bits/Row_meat.hpp             |   72 ++
 inst/include/armadillo_bits/arma_static_assert.hpp   |   16 
 inst/include/armadillo_bits/arma_version.hpp         |    8 
 inst/include/armadillo_bits/auxlib_bones.hpp         |    6 
 inst/include/armadillo_bits/auxlib_meat.hpp          |  291 +++++++++++
 inst/include/armadillo_bits/config.hpp               |   16 
 inst/include/armadillo_bits/diskio_meat.hpp          |    4 
 inst/include/armadillo_bits/fn_as_scalar.hpp         |    8 
 inst/include/armadillo_bits/fn_norm.hpp              |  186 +++++--
 inst/include/armadillo_bits/fn_svd.hpp               |   47 +
 inst/include/armadillo_bits/fn_toeplitz.hpp          |   18 
 inst/include/armadillo_bits/glue_relational_meat.hpp |  345 ++++----------
 inst/include/armadillo_bits/glue_times_meat.hpp      |    8 
 inst/include/armadillo_bits/glue_toeplitz_bones.hpp  |   15 
 inst/include/armadillo_bits/glue_toeplitz_meat.hpp   |   82 +++
 inst/include/armadillo_bits/op_strans_meat.hpp       |   44 +
 inst/include/armadillo_bits/promote_type.hpp         |  241 +++++----
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 inst/include/armadillo_bits/subview_bones.hpp        |   13 
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 inst/include/armadillo_bits/subview_cube_meat.hpp    |    8 
 inst/include/armadillo_bits/subview_meat.hpp         |   96 +++
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 33 files changed, 1566 insertions(+), 737 deletions(-)

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New package mvtsplot with initial version 1.0
Package: mvtsplot
Version: 1.0
Date: 2011-07-21
Depends: R (>= 2.13.0), methods, splines, RColorBrewer
Title: Multivariate Time Series Plot
Author: Roger D. Peng
Maintainer: Roger D. Peng
Description: A function for plotting multivariate time series data
License: GPL (>= 2)
Packaged: 2011-07-21 18:01:28 UTC; rdpeng
Repository: CRAN
Date/Publication: 2011-07-23 13:58:06

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Package mvabund updated to version 2.2-5.6 with previous version 2.2-5.3 dated 2011-07-06

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 2.2-5.3 dated 2011-07-06 and 2.2-5.6 dated 2011-07-23

 DESCRIPTION                       |    8 +--
 R/anova.manyglm.R                 |   37 ++++++++------
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 28 files changed, 246 insertions(+), 269 deletions(-)

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Package multcomp updated to version 1.2-7 with previous version 1.2-6 dated 2011-05-02

Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
Author: Torsten Hothorn, Frank Bretz and Peter Westfall and Richard M. Heiberger and Andre Schuetzenmeister
Maintainer: Torsten Hothorn

Diff between multcomp versions 1.2-6 dated 2011-05-02 and 1.2-7 dated 2011-07-23

 DESCRIPTION                    |    8 ++--
 NEWS                           |    6 +++
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Package monomvn updated to version 1.8-6 with previous version 1.8-5 dated 2011-03-08

Title: Estimation for multivariate normal and Student-t data with monotone missingness
Description: Estimation of multivariate normal and student-t data of arbitrary dimension where the pattern of missing data is monotone. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle a nearly arbitrary amount of missing data. The current version supports maximum likelihood inference and a full Bayesian approach employing scale-mixtures for the lasso (double-exponential) and Normal-Gamma priors, and Student-t errors. Monotone data augmentation extends this Bayesian approach to arbitrary missingness patterns. A fully functional standalone interface to the Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown), and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy

Diff between monomvn versions 1.8-5 dated 2011-03-08 and 1.8-6 dated 2011-07-23

 ChangeLog     |    7 ++++
 DESCRIPTION   |    8 ++---
 R/blasso.R    |    9 +++--
 man/blasso.Rd |    6 ++-
 src/blasso.cc |   19 +++++++-----
 src/matrix.c  |   89 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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New package motmot with initial version 1.0.1
Package: motmot
Type: Package
Title: Models of Trait Macroevolution on Trees
Version: 1.0.1
Depends: R (>= 2.10.0), ape, mvtnorm, MASS, caper, laser
Date: 2011-07-08
Author: Gavin Thomas, Rob Freckleton
Maintainer: Gavin Thomas
Description: motmot provides functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions are based around tests of variation in the rates of trait evolution.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: motmot
URL: http://seis.bris.ac.uk/~gt0027/code.html
Repository/R-Forge/Revision: 26
Date/Publication: 2011-07-23 13:57:40
Packaged: 2011-07-08 21:05:03 UTC; rforge

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Package mixsep updated to version 0.1-6 with previous version 0.1-5 dated 2011-05-26

Title: Forensic Genetics DNA Mixture Separation
Description: Separates DNA mixtures using a statistical model within a greedy algorithm.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink

Diff between mixsep versions 0.1-5 dated 2011-05-26 and 0.1-6 dated 2011-07-23

 DESCRIPTION      |    8 ++++----
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Package mirt updated to version 0.1-14 with previous version 0.1-13 dated 2011-07-02

Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polychotomous response data using latent trait models under the Item Response Theory paradigm. Includes the multivariate two- and three-parameter logistic models, confirmatory bifactor analysis, and polytomous confirmatory and exploratory item response models.
Author: Phil Chalmers
Maintainer: Phil Chalmers

Diff between mirt versions 0.1-13 dated 2011-07-02 and 0.1-14 dated 2011-07-23

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 mirt-0.1-14/mirt/man/polymirt.Rd     |   40 ++--------
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 mirt-0.1-14/mirt/src/dgroup.c        |   28 +++++++
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New package minimax with initial version 1.0
Package: minimax
Type: Package
Title: Minimax distribution family
Version: 1.0
Date: 2011-07-22
Author: Bill Venables
Maintainer: Bill Venables
Description: The minimax family of distributions is a two-parameter family like the beta family, but computationally a lot more tractible.
License: GPL-2 | GPL-3
LazyLoad: yes
Packaged: 2011-07-22 05:11:31 UTC; ven037
Repository: CRAN
Date/Publication: 2011-07-23 13:57:15

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Package mefa4 updated to version 0.2-2 with previous version 0.2-1 dated 2011-05-15

Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package using sparse matrices for enhanced efficiency. Sparse array-like obejects are supported via lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos

Diff between mefa4 versions 0.2-1 dated 2011-05-15 and 0.2-2 dated 2011-07-23

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 mefa4-0.2-2/mefa4/man/Mefa.Rd          |    6 
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Package mc2d updated to version 0.1-10 with previous version 0.1-9 dated 2010-12-17

Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: Various distributions and utilities to ease the use of R to build and study Two-Dimensional Monte-Carlo simulations
Author: Regis Pouillot , Marie Laure Delignette-Muller and Jean-Baptiste Denis
Maintainer: Regis Pouillot

Diff between mc2d versions 0.1-9 dated 2010-12-17 and 0.1-10 dated 2011-07-23

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 mc2d-0.1-10/mc2d/R/betagen.R                |   54 +++-
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 mc2d-0.1-10/mc2d/R/empiricalD.R             |   35 ++-
 mc2d-0.1-10/mc2d/R/extractvar.R             |    2 
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 mc2d-0.1-10/mc2d/R/rdirichlet.R             |   27 +-
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Package matlab updated to version 0.8.7 with previous version 0.8.6 dated 2011-04-24

Title: MATLAB emulation package
Description: Emulate MATLAB code using R
Author: P. Roebuck
Maintainer: P. Roebuck

Diff between matlab versions 0.8.6 dated 2011-04-24 and 0.8.7 dated 2011-07-23

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Package lmomco updated to version 1.4.2 with previous version 1.3.6 dated 2011-06-25

Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
Description: The package implements the statistical theory of L-moments in R including L-moment estimation, probability-weighted moment estimation, parameter estimation for numerous familiar and not-so-familiar distributions, and L-moment estimation for the same distributions from the parameters. L-moments are derived from the expectations of order statistics and are linear with respect to the probability-weighted moments; choice of either can be made by mathematical convenience. L-moments are directly analogous to the well-known product moments; however, L-moments have many advantages including unbiasedness, robustness, and consistency with respect to the product moments. The method of L-moments can out perform the method of maximum likelihood. The lmomco package historically is oriented around canonical FORTRAN algorithms of J.R.M. Hosking, and the nomenclature for many of the functions parallels that of the Hosking library, which later became available in the lmom package. However, vast arrays of various extensions and curiosities are added by the author to aid and expand the breadth of L-moment application. Such extensions include venerable statistics as Sen weighted mean, Gini mean difference, plotting positions, and conditional probability adjustment. The plotting of L-moment ratio diagrams is directly supported in this package. Computations of L-moments for right-tail and left-tail censoring by known or unknown censoring threshold and also by indicator variable also are available. E.A.H. Elamir and A.H. Seheult have developed the trimmed L-moments, which are implemented in this package, and numerical integration of quantile functions is used to dynamically compute trajectories of select TL-moment ratios for the construction of TL-moment ratio diagrams. Robert Serfling and Peng Xiao have extended L-moments into multivariate space; the so-called sample L-comoments are implemented here and might have considerable application in copula theory because they measure asymmetric correlation and higher co-moments. The supported distributions with moment type shown as "L" (L-moments) or "TL" (trimmed L-moments) and additional support for right-tail censoring ([RC]) include: Cauchy (TL), Exponential (L), Gamma (L), Generalized Extreme Value (L), Generalized Lambda (L & TL), Generalized Logistic (L), Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel (L), Kappa (L), Kumaraswamy (L), Normal (L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L), Wakeby (L), and Weibull (L).
Author: William H. Asquith
Maintainer: William H. Asquith

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Package lme4 updated to version 0.999375-40 with previous version 0.999375-39 dated 2011-03-08

Title: Linear mixed-effects models using S4 classes
Description: Fit linear and generalized linear mixed-effects models.
Author: Douglas Bates , Martin Maechler and Ben Bolker
Maintainer:

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Package linkcomm updated to version 1.0-3 with previous version 1.0-2 dated 2011-05-29

Title: Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Description: Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type.
Author: Alex T. Kalinka
Maintainer: Alex T. Kalinka

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Package lessR updated to version 2.0 with previous version 1.9.8 dated 2011-06-30

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, rad() and full(), together read the csv data and generate descriptive statistics for all variables in the data frame, plus histograms and bar charts for all respective numerical and non-numerical variables. The function smd.t.test introduces the ODDSMD plot, which displays the Overlapping Density Distributions of two independent groups as well as a visual display of the mean difference and standardized mean difference. Other functions provide for descriptive statistics, the t-test from descriptive statistics, a comprehensive regression analysis, color plotting, color bar chart, color histogram, color box plot, density curves, a calibrated power curve plotted with colors, and the reading and display of csv formatted data. The function help.me provides a help system that suggests specific analyses and functions.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing

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Package itsmr updated to version 1.1 with previous version 1.0 dated 2011-06-15

Title: Time series analysis package for students
Description: This package provides a subset of the functionality found in the Windows-based program ITSM. The intended audience is students using the textbook "Introduction to Time Series and Forecasting" by Peter J. Brockwell and Richard A. Davis.
Author: George Weigt
Maintainer: George Weigt

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New package kinship2 with initial version 1.2.1
Package: kinship2
Version: 1.2.1
Date: 2011-7-21
Title: Pedigree functions
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Martha Matsumoto, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell
Depends: Matrix, quadprog
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.
License: GPL (>= 2)
URL: http://r-forge.r-project.org
Packaged: 2011-07-21 21:20:45 UTC; sinnwell
Repository: CRAN
Date/Publication: 2011-07-23 13:55:47

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Package iterators updated to version 1.0.5 with previous version 1.0.4 dated 2011-05-20

Title: Iterator construct for R
Description: Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.
Author: Revolution Analytics
Maintainer: Revolution Analytics

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New package isopat with initial version 1.0
Package: isopat
Type: Package
Title: Calculation of isotopic pattern for a given molecular formula
Version: 1.0
Date: 2011-04-05
Author: Martin Loos
Maintainer: Martin Loos
Description: The function calculates the isotopic pattern (fine structures) for a given chemical formula.
License: GPL-2
LazyLoad: yes
Packaged: 2011-07-07 09:35:25 UTC; loosmart
Repository: CRAN
Date/Publication: 2011-07-23 13:55:33

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Package isdals updated to version 1.0-4 with previous version 1.0-2 dated 2011-02-22

Title: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Description: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Author: Claus Ekstrom and Helle Sorensen
Maintainer: Claus Ekstrom

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Package iplots updated to version 1.1-4 with previous version 1.1-3 dated 2009-02-07

Title: iPlots - interactive graphics for R
Description: Interactive plots for R
Author: Simon Urbanek , Tobias Wichtrey
Maintainer: Simon Urbanek

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Package idr updated to version 1.1 with previous version 1.0 dated 2011-06-15

Title: Irreproducible discovery rate
Description: This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, by Li, Brown, Huang, and Bickel
Author: Qunhua Li
Maintainer: Qunhua Li

Diff between idr versions 1.0 dated 2011-06-15 and 1.1 dated 2011-07-23

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Package huge updated to version 1.1.0 with previous version 1.0.3 dated 2011-06-17

Title: High-dimensional Undirected Graph Estimation
Description: The package "huge" provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline. In preprocessing stage, the nonparanormal(npn) transformation is applied to help relax the normality assumption. In the graph estimation stage, the graph structure is estimated by Meinshausen-Buhlmann graph estimation or the graphical lasso, and both methods can be further accelerated by the lossy screening rule preselecting the neighborhood of each variable by correlation thresholding. We target on high-dimensional data analysis usually d >> n, and the computation is memory-optimized using the sparse matrix output. We also provide a computationally efficient approach, correlation thresholding graph estimation. Three regularization/thresholding parameter selection methods are included in this package: (1)stability approach for regularization selection (2) rotation information criterion (3) extended Bayesian information criterion which is only available for the graphical lasso.
Author: Tuo Zhao, Han Liu, Kathryn Roeder, John Lafferty, Larry Wasserman
Maintainer: Tuo Zhao , Han Liu

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Package googleVis updated to version 0.2.7 with previous version 0.2.6 dated 2011-06-15

Title: Interface between R and the Google Visualisation API
Description: googleVis provides an interface between R and the Google Visualisation API to create interactive charts for web pages. The functions of the package allow the user to visualise data stored in R data frames with the Google Visualisation API without uploading their data to Google. The output of a googleVis function is html code that contains the data and references to JavaScript functions hosted by Google and can be displayed locally with the R HTTP help server. A browser with Flash and Internet connection is required. Please visit the project web site for more information and examples.
Author: Markus Gesmann, Diego de Castillo
Maintainer: Markus Gesmann

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Package glmpathcr updated to version 1.0.2 with previous version 1.0.1 dated 2011-03-16

Title: Fit a penalized continuation ratio model for predicting an ordinal response.
Description: Provides a function for fitting a penalized constrained continuation ratio model using the glmpath algorithm and methods for extracting coefficient estimates, predicted class, class probabilities, and plots.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer

Diff between glmpathcr versions 1.0.1 dated 2011-03-16 and 1.0.2 dated 2011-07-23

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Package glmnetcr updated to version 1.0.1 with previous version 1.0 dated 2011-03-16

Title: Fit a penalized constrained continuation ratio model for predicting an ordinal response
Description: This packages includes functions for restructuring an ordinal response dataset for fitting continuation ratio models for datasets where the number of covariates exceeds the sample size or when there is collinearity among the covariates. This package uses the glmnet package fitting algorithm.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer

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Package geophys updated to version 1.2-0 with previous version 1.1-0 dated 2010-11-24

Title: Geophysics, Continuum Mechanics, Mogi Model
Description: Geophysics, Continuum Mechanics, Mogi Model, Okada Model
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between geophys versions 1.1-0 dated 2010-11-24 and 1.2-0 dated 2011-07-23

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New package glm2 with initial version 1.0
Package: glm2
Type: Package
Title: Fitting Generalized Linear Models
Version: 1.0
Date: 2011-07-22
Author: Ian Marschner (using code from glm and glm.fit in the stats package)
Maintainer: Ian Marschner
Depends: R (>= 2.12.1), stats
Description: Fits generalized linear models using the same model specification as glm in the stats package, but with a modified default fitting method that provides greater stability for models that may fail to converge using glm
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2011-07-22 03:14:43 UTC; imarschn
Repository: CRAN
Date/Publication: 2011-07-23 13:53:05

More information about glm2 at CRAN
Permanent link

Package gamm4 updated to version 0.1-3 with previous version 0.1-2 dated 2011-03-02

Title: Generalized additive mixed models using mgcv and lme4
Description: Fit generalized additive mixed models via a version of mgcv's gamm function, using lme4 for estimation via Fabian Scheipl's trick.
Author: Simon Wood
Maintainer: Simon Wood

Diff between gamm4 versions 0.1-2 dated 2011-03-02 and 0.1-3 dated 2011-07-23

 DESCRIPTION |    6 ++---
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Package gWidgetstcltk updated to version 0.0-44 with previous version 0.0-43 dated 2011-04-30

Title: Toolkit implementation of gWidgets for tcltk package
Description: Port of the gWidgets API to the tcltk package. Requires TK 8.5 or greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml. This is the default on Windows. Under linux, Tk must be installed. Under Mac OS X (10.5) there are two options: native Tk or X11. For the native one, Tk must be upgraded. See www.tcl.tk to download source. Under the Mac it compiles and installs cleanly. For X11, tcltk libraries can be downloaded to augment the R binary package. See http://cran.r-project.org/bin/macosx/tools/. The gdf function requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
Author: John Verzani
Maintainer: John Verzani

Diff between gWidgetstcltk versions 0.0-43 dated 2011-04-30 and 0.0-44 dated 2011-07-23

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Package gWidgetsRGtk2 updated to version 0.0-75 with previous version 0.0-74 dated 2011-05-08

Title: Toolkit implementation of gWidgets for RGtk2
Description: Port of gWidgets API to RGtk2
Author: Michael Lawrence, John Verzani
Maintainer: John Verzani

Diff between gWidgetsRGtk2 versions 0.0-74 dated 2011-05-08 and 0.0-75 dated 2011-07-23

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Package gWidgets updated to version 0.0-45 with previous version 0.0-44 dated 2011-04-30

Title: gWidgets API for building toolkit-independent, interactive GUIs
Description: gWidgets provides a toolkit-independent API for building interactive GUIs. Atleast one of the gWidgetsXXX packages, such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project http://scigraphica.sourceforge.net.
Author: John Verzani. Based on the iwidgets code of Simon Urbanek and suggestions by Simon Urbanek, Philippe Grosjean and Michael Lawrence
Maintainer: John Verzani

Diff between gWidgets versions 0.0-44 dated 2011-04-30 and 0.0-45 dated 2011-07-23

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New package gRim with initial version 0.1.0
Package: gRim
Version: 0.1.0
Title: Graphical Interaction Models
Author: Sren Hjsgaard
Maintainer: Sren Hjsgaard
Description: Implements graphical interaction models for contingency tables (i.e. log-linear models) and graphical Gaussian models for the multivariate normal data (i.e. covariance selection models).
License: GPL (>= 2)
URL: http://genetics.agrsci.dk/~sorenh/public/R/gRim/
Depends: R (>= 2.1.0),methods,gRbase,graph,gRain,RBGL,igraph,doBy
Encoding: latin1
Suggests: Rgraphviz
Packaged: 2011-07-19 22:39:33 UTC; SHD
Repository: CRAN
Date/Publication: 2011-07-23 13:52:24

More information about gRim at CRAN
Permanent link

Package gRbase updated to version 1.4.0 with previous version 1.3.9 dated 2011-01-18

Title: A package for graphical modelling in R
Description: The gRbase package provides certain general constructs which are used by other graphical modelling packages. This includes 1) the concept of gmData (graphical meta data), 2) several graph algorithms 3) facilities for table operations, 4) functions for testing for conditional independence. gRbase also illustrates how hierarchical log-linear models (hllm) may be implemented.
Author: Sren Hjsgaard and Claus Dethlefsen with contributions from Clive Bowsher
Maintainer: Sren Hjsgaard

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Package gRain updated to version 0.8.8 with previous version 0.8.7 dated 2011-01-18

Title: Graphical Independence Networks
Description: A package for probability propagation in graphical independence networks, also known as probabilistic expert systems (which includes Bayesian networks as a special case).
Author: Sren Hjsgaard
Maintainer: Sren Hjsgaard

Diff between gRain versions 0.8.7 dated 2011-01-18 and 0.8.8 dated 2011-07-23

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Package filehash updated to version 2.2 with previous version 2.1-1 dated 2010-10-05

Title: Simple key-value database
Description: Simple key-value database
Author: Roger D. Peng
Maintainer: Roger D. Peng

Diff between filehash versions 2.1-1 dated 2010-10-05 and 2.2 dated 2011-07-23

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Package extRemes updated to version 1.63 with previous version 1.62 dated 2010-04-25

Title: Extreme value toolkit.
Description: Uses Stuart Coles' (Coles, Stewart, "An introduction to statistical modeling of extreme values", Springer-Verlag, London 2001) S-plus functions as ported to the R programming language (ismev) by Alec Stephenson (http://www.maths.lancs.ac.uk/~stephena/). This toolkit provides a Graphical User Interface (GUI) to ismev for pedagogical purposes.
Author: Eric Gilleland, Rick Katz, Greg Young
Maintainer: Eric Gilleland

Diff between extRemes versions 1.62 dated 2010-04-25 and 1.63 dated 2011-07-23

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New package fdrci with initial version 1.0
Package: fdrci
Type: Package
Title: Permutation-based FDR Point and Confidence Interval Estimation
Version: 1.0
Date: 2011-06-18
Author: Joshua Millstein
Maintainer: Joshua Millstein
Description: FDR functions for permutation-based estimators, including pi0 as well as FDR confidence intervals. The confidence intervals account for dependencies between tests by the incorporation of an overdispersion parameter, which is estimated from the permuted data.
License: Artistic-2.0
LazyLoad: yes
Packaged: 2011-06-24 21:37:20 UTC; jmillste
Repository: CRAN
Date/Publication: 2011-07-23 13:51:56

More information about fdrci at CRAN
Permanent link

Package expsmooth updated to version 2.01 with previous version 2.00 dated 2009-09-07

Title: Data sets from "Forecasting with exponential smoothing"
Description: Data sets from the book "Forecasting with exponential smoothing: the state space approach" by Hyndman, Koehler, Ord and Snyder (Springer, 2008).
Author: Rob J Hyndman
Maintainer: Rob J Hyndman

Diff between expsmooth versions 2.00 dated 2009-09-07 and 2.01 dated 2011-07-23

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Package epicalc updated to version 2.13.1.0 with previous version 2.12.2.3 dated 2011-04-11

Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
Author: Virasakdi Chongsuvivatwong
Maintainer: Virasakdi Chongsuvivatwong

Diff between epicalc versions 2.12.2.3 dated 2011-04-11 and 2.13.1.0 dated 2011-07-23

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Package editrules updated to version 0.9-0 with previous version 0.8 dated 2011-07-06

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

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Package earth updated to version 3.2-1 with previous version 3.2-0 dated 2011-06-19

Title: Multivariate Adaptive Regression Spline Models
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is copyrighted and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani.
Maintainer: Stephen Milborrow

Diff between earth versions 3.2-0 dated 2011-06-19 and 3.2-1 dated 2011-07-23

 DESCRIPTION                         |    6 -
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More information about earth at CRAN
Permanent link

Package delftfews updated to version 0.3-67 with previous version 0.3-38 dated 2010-08-27

Title: delftfews R extensions
Description: a collection of timeseries sets handling functions used here at work (Nelen en Schuurmans), initially for the Lizard Scripter.
Author: Mario Frasca , Michel van Leeuwen
Maintainer: Mario Frasca

Diff between delftfews versions 0.3-38 dated 2010-08-27 and 0.3-67 dated 2011-07-23

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Package ddepn updated to version 1.9 with previous version 1.8 dated 2011-06-17

Title: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.
Description: DDEPN (Dynamic Deterministic Effects Propagation Networks): Infer signalling networks for timecourse data. Given a matrix of high-throughput genomic or proteomic timecourse data, generated after external perturbation of the biological system, DDEPN models the time-dependent propagation of active and passive states depending on a network structure. Optimal network structures given the experimental data are reconstructed. Two network inference algorithms can be used: inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA, a Genetic Algorithm network optimisation. Inclusion of prior biological knowledge can be done using different network prior models.
Author: Christian Bender
Maintainer: Christian Bender

Diff between ddepn versions 1.8 dated 2011-06-17 and 1.9 dated 2011-07-23

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Package dclone updated to version 1.3-3 with previous version 1.3-2 dated 2011-05-15

Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods with support for JAGS, WinBUGS and OpenBUGS. With some functions for parallel MCMC computations.
Author: Peter Solymos
Maintainer: Peter Solymos

Diff between dclone versions 1.3-2 dated 2011-05-15 and 1.3-3 dated 2011-07-23

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Package cts updated to version 1.0-4 with previous version 1.0-1 dated 2006-09-29

Title: Continuous Time Autoregressive Models
Description: Continuous Time Autoregressive Models and the Kalman Filter
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port by Zhu Wang.
Maintainer: Zhu Wang

Diff between cts versions 1.0-1 dated 2006-09-29 and 1.0-4 dated 2011-07-23

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Package circular updated to version 0.4-3 with previous version 0.4-2 dated 2011-03-19

Title: Circular Statistics
Description: Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
Author: Ulric Lund , Claudio Agostinelli
Maintainer: Claudio Agostinelli

Diff between circular versions 0.4-2 dated 2011-03-19 and 0.4-3 dated 2011-07-23

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Package care updated to version 1.1.0 with previous version 1.0.0 dated 2010-08-08

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the CAR regression approach described in Zuber and Strimmer (2011). CAR scores measure the correlations between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables - see Zuber and Strimmer (2011) for details. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.0.0 dated 2010-08-08 and 1.1.0 dated 2011-07-23

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Package cacheSweave updated to version 0.6 with previous version 0.5 dated 2011-06-30

Title: Tools for caching Sweave computations
Description: Tools for caching Sweave computations and storing them in key-value databases
Author: Roger D. Peng , with contributions from Tobias Abenius
Maintainer: Roger D. Peng

Diff between cacheSweave versions 0.5 dated 2011-06-30 and 0.6 dated 2011-07-23

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Package bios2mds updated to version 1.1 with previous version 1.0 dated 2011-07-05

Title: From BIOlogical Sequences to MultiDimensional Scaling
Description: Bios2mds is primarily dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.
Author: Julien Pele with Jean-Michel Becu, Herve Abdi, and Marie Chabbert
Maintainer: Marie Chabbert

Diff between bios2mds versions 1.0 dated 2011-07-05 and 1.1 dated 2011-07-23

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Package basicspace updated to version 0.03 with previous version 0.02 dated 2011-01-26

Title: A Package to Recover a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling (SVD generalization with missing values)
Author: Keith Poole , Howard Rosenthal , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: Keith Poole

Diff between basicspace versions 0.02 dated 2011-01-26 and 0.03 dated 2011-07-23

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Package biglm updated to version 0.8 with previous version 0.7 dated 2009-05-05

Title: bounded memory linear and generalized linear models
Description: Regression for data too large to fit in memory
Author: Thomas Lumley
Maintainer: Thomas Lumley

Diff between biglm versions 0.7 dated 2009-05-05 and 0.8 dated 2011-07-23

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Package automap updated to version 1.0-11 with previous version 1.0-10 dated 2011-05-30

Title: Automatic interpolation package
Description: This package performs an automatic interpolation by automatically estimating the variogram and then calling gstat.
Author: Paul Hiemstra
Maintainer: Paul Hiemstra

Diff between automap versions 1.0-10 dated 2011-05-30 and 1.0-11 dated 2011-07-23

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New package auteur with initial version 0.11.0612
Package: auteur
Type: Package
Title: Bayesian sampler of the trait-evolutionary process
Version: 0.11.0612
Date: 2011-06-12
Author: JM Eastman, ME Alfaro, AL Hipp, P Joyce, Matthew Pennell, and LJ Harmon
Maintainer: Jonathan Eastman
Depends: ape, geiger, colorspace, Rcpp
LinkingTo: Rcpp
Description: Identifies shifts in process of continuous-trait evolution on phylogenetic trees
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2011-07-08 17:03:02 UTC; jeastman
Repository: CRAN
Date/Publication: 2011-07-23 13:49:54

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Package aroma.cn updated to version 0.8.0 with previous version 0.7.3 dated 2011-06-25

Title: Copy-number analysis of large microarray data sets
Description: Package for analysis of copy-number estimates obtained from various platforms.
Author: Henrik Bengtsson and Pierre Neuvial
Maintainer: Henrik Bengtsson

Diff between aroma.cn versions 0.7.3 dated 2011-06-25 and 0.8.0 dated 2011-07-23

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Package animation updated to version 2.0-5 with previous version 2.0-4 dated 2011-04-28

Title: A Gallery of Animations in Statistics and Utilities to Create Animations
Description: This package contains various functions for animations in statistics, covering many areas such as probability theory, mathematical statistics, multivariate statistics, nonparametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions might be of help in teaching statistics and data analysis. Also provided in this package are several approaches to save animations to various formats, e.g. Flash, GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(), saveLatex(), and saveVideo() respectively). PDF animations can be inserted into Sweave easily.
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between animation versions 2.0-4 dated 2011-04-28 and 2.0-5 dated 2011-07-23

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Package adabag updated to version 2.0 with previous version 1.1 dated 2007-10-25

Title: Applies Adaboost.M1 and Bagging
Description: This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation predictions can be done. This version 2.0 adds a new function "margins" to calculate the margins for these classifiers. Also a higher flexibility is achieved giving access to the "rpart.control" argument of "rpart".
Author: Esteban Alfaro Cortes, Matias Gamez Martinez and Noelia Garcia Rubio
Maintainer: Esteban Alfaro Cortes

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Package zoo updated to version 1.7-2 with previous version 1.7-1 dated 2011-07-18

Title: S3 Infrastructure for Regular and Irregular Time Series (Z's ordered observations)
Description: An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis

Diff between zoo versions 1.7-1 dated 2011-07-18 and 1.7-2 dated 2011-07-23

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Package VIM updated to version 2.0.3 with previous version 2.0.2 dated 2011-07-02

Title: Visualization and Imputation of Missing Values
Description: This package introduces new tools for the visualization of missing values in R, which can be used for exploring the data and the structure of the missing values. Depending on this structure, they may help to identify the mechanism generating the missings. A graphical user interface allows an easy handling of the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik
Maintainer: Matthias Templ

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Package TreePar updated to version 2.1 with previous version 1.4 dated 2011-05-10

Title: Estimating speciation and extinction rates based on phylogenies
Description: For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (i) as a function of time, i.e. rate shifts at specified times or mass extinction events (implemented as bd.shifts.optim) or (ii) as a function of the number of species, i.e. density-dependence (implemented as bd.densdep.optim). Note that the method takes into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. For a given phylogeny on higher taxa, but where the number of species is known within each higher taxa, speciation and extinction rates can be estimated, under the assumption that these rates remained constant (implemented as bd.groups.optim).
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreePar versions 1.4 dated 2011-05-10 and 2.1 dated 2011-07-23

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Package SamplingStrata updated to version 0.9-1 with previous version 0.9 dated 2011-04-29

Title: Optimal stratification of sampling frames for multipurpose sampling surveys
Description: In the field of sampling design (in particular for stratified sampling), this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample size under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated by calculating (using the Bethel-Chromy algorithm) the sampling size satisfying accuracy constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. There is also a function that allows to build the most important input to the optimisation step, i.e. the "strata" dataframe, containing information (means and standard errors) regarding the distributions of the target variables in the different strata, using the sampling frame or using data from previous rounds of the same survey.
Author: Giulio Barcaroli
Maintainer: Giulio Barcaroli

Diff between SamplingStrata versions 0.9 dated 2011-04-29 and 0.9-1 dated 2011-07-23

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Permanent link

Package SYNCSA updated to version 1.1 with previous version 1.0 dated 2011-05-25

Title: SYNCSA - Analysis of functional and phylogenetic patterns in metacommunities.
Description: Analysis of metacommunities based on functional traits and phylogeny of the community components. The functions that are offered here implement for the R environment methods that have been available in the SYNCSA application written in C++ (by Valerio Pillar, available at http://ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani

Diff between SYNCSA versions 1.0 dated 2011-05-25 and 1.1 dated 2011-07-23

 DESCRIPTION           |    6 +++---
 R/matrix.x.R          |    2 +-
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Permanent link

Package SPOT updated to version 0.1.1550 with previous version 0.1.1375 dated 2011-05-03

Title: Sequential Parameter Optimization
Description: R-Package for Sequential Parameter Optimization Toolbox
Author: T. Bartz-Beielstein with contributions from: J. Ziegenhirt, W. Konen, O. Flasch, P. Koch, M. Zaefferer
Maintainer: M. Zaefferer

Diff between SPOT versions 0.1.1375 dated 2011-05-03 and 0.1.1550 dated 2011-07-23

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More information about SPOT at CRAN
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Package SPARQL updated to version 1.2 with previous version 1.1 dated 2011-06-22

Title: SPARQL client
Description: Load SPARQL result table from an end-point as a data.frame
Author: Willem Robert van Hage and Tomi Kauppinen , with contributions from Christopher Davis
Maintainer: Willem Robert van Hage and Tomi Kauppinen

Diff between SPARQL versions 1.1 dated 2011-06-22 and 1.2 dated 2011-07-23

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More information about SPARQL at CRAN
Permanent link

Package ResourceSelection updated to version 0.1-1 with previous version 0.1-0 dated 2011-06-04

Title: Resource Selection (Probability) Functions for Use-Availability Data
Description: Resource Selection (Probability) Functions for use-availability wildlife data as described in Lele and Keim (2006, Ecology 87, 3021--3028), and Lele (2009, J. Wildlife Management 73, 122--127).
Author: Subhash R. Lele, Jonah L. Keim, Peter Solymos
Maintainer: Peter Solymos

Diff between ResourceSelection versions 0.1-0 dated 2011-06-04 and 0.1-1 dated 2011-07-23

 DESCRIPTION          |    8 ++++----
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Package RcppArmadillo updated to version 0.2.26 with previous version 0.2.25 dated 2011-06-30

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 2.0.2). 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 0.2.25 dated 2011-06-30 and 0.2.26 dated 2011-07-23

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Permanent link

Package RcmdrPlugin.DoE updated to version 0.10-4 with previous version 0.10-2 dated 2011-02-21

Title: R Commander Plugin for (industrial) Design of Experiments
Description: WARNING: This package is currently in beta status! The package provides a platform-independent GUI for design of experiments. It is implemented as a plugin to the R-Commander, which is a more general graphical user interface for statistics in R based on tcl/tk. DoE functionality can be accessed through the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping

Diff between RcmdrPlugin.DoE versions 0.10-2 dated 2011-02-21 and 0.10-4 dated 2011-07-23

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Package RVAideMemoire updated to version 0.9-5 with previous version 0.9.1 dated 2011-03-14

Title: Diverse basic statistical and graphical functions accompanying the french book 'Aide-memoire de statistique appliquee a la biologie'
Description: This package contains diverse more or less complicated functions, written to simplify beginners' life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools... All functions are presented in the french book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Herv
Maintainer: Maxime Herv

Diff between RVAideMemoire versions 0.9.1 dated 2011-03-14 and 0.9-5 dated 2011-07-23

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New package RXKCD with initial version 1.0
Package: RXKCD
Type: Package
Title: Get XKCD comic from R
Version: 1.0
Date: 2011-06-19
Author:
Maintainer:
Description: This package allows the visualization of your favorite XKCD comic strip directly from R
Depends: R (>= 2.11.0), RJSONIO, png, ReadImages
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: rxkcd
Repository/R-Forge/Revision: 3
Date/Publication: 2011-07-23 13:04:00
Packaged: 2011-07-13 20:43:23 UTC; rforge

More information about RXKCD at CRAN
Permanent link

Package RPMG updated to version 2.0-6 with previous version 2.0-5 dated 2010-11-24

Title: Graphical User Interface (GUI) for interactive R analysis sessions
Description: Poor Man's Gui: create interactive R analysis sessions
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between RPMG versions 2.0-5 dated 2010-11-24 and 2.0-6 dated 2011-07-23

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Package RH2 updated to version 0.1-2.5 with previous version 0.1-2.3 dated 2011-03-08

Title: DBI/RJDBC interface to h2 Database
Description: DBI/RJDBC interface to h2 database. h2 version 1.3.155 is included.
Author: G. Grothendieck. Author of h2 is Thomas Mueller.
Maintainer: G. Grothendieck

Diff between RH2 versions 0.1-2.3 dated 2011-03-08 and 0.1-2.5 dated 2011-07-23

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Package R.oo updated to version 1.8.1 with previous version 1.8.0 dated 2011-04-04

Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.oo versions 1.8.0 dated 2011-04-04 and 1.8.1 dated 2011-07-23

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Package R.cache updated to version 0.4.3 with previous version 0.4.2 dated 2011-05-21

Title: Fast and light-weight caching (memoization) of objects
Description: Methods for memoization, that is, caching arbitrary R objects in persistent memory. Objects can be loaded and saved stratified on a set of hashing objects.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.cache versions 0.4.2 dated 2011-05-21 and 0.4.3 dated 2011-07-23

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Package QTLRel updated to version 0.2-9 with previous version 0.2-8 dated 2011-06-28

Title: Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng
Maintainer: Riyan Cheng

Diff between QTLRel versions 0.2-8 dated 2011-06-28 and 0.2-9 dated 2011-07-23

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Package ProjectTemplate updated to version 0.3-5 with previous version 0.3-4 dated 2011-07-04

Title: Automates the creation of new statistical analysis projects.
Description: ProjectTemplate provides functions to automatically build a directory structure for a new R project. Using this structure, ProjectTemplate automates data loading, preprocessing, library importing and unit testing.
Author: John Myles White
Maintainer: John Myles White

Diff between ProjectTemplate versions 0.3-4 dated 2011-07-04 and 0.3-5 dated 2011-07-23

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Package Peak2Trough updated to version 1.1 with previous version 1.0 dated 2011-04-28

Title: Estimation of the peak-to-trough ratio of a seasonal variation component
Description: Estimation of the peak-to-trough ratio of a seasonal variation component.
Author: Anette Luther Christensen
Maintainer: Anette Luther Christensen

Diff between Peak2Trough versions 1.0 dated 2011-04-28 and 1.1 dated 2011-07-23

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Package PSCBS updated to version 0.11.7 with previous version 0.11.3 dated 2011-07-07

Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segments allele-specific DNA copy number data to detect regions with abnormal copy number within each parental chromosome
Author: A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A. Olshen, V.E. Seshan
Maintainer: Henrik Bengtsson

Diff between PSCBS versions 0.11.3 dated 2011-07-07 and 0.11.7 dated 2011-07-23

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New package OpenRepGrid with initial version 0.1.5
Package: OpenRepGrid
Maintainer: Mark Heckmann
License: GPL (>= 2)
Title: Tools to analyse repertory grid data
LazyData: yes
Type: Package
LazyLoad: yes
Author: Mark Heckmann
Description: Tools to analyse repertory grid data
Version: 0.1.5
Date: 2011-07-03
Depends: methods, grid, colorspace, plyr, abind, rgl, psych, XML, tcltk
Collate: 'bertin.r' 'calc.r' 'data-openrepgrid.r' 'dev-functions.r' 'export.r' 'gmMain.r' 'import.r' 'measures.r' 'openrepgrid.r' 'repgrid.r' 'repgrid-basicops.r' 'repgrid-constructs.r' 'repgrid-elements.r' 'repgrid-output.r' 'repgrid-plots.r' 'repgrid-ratings.r' 'rgl-3d.r' 'utils-import.r' 'utils.r' 'zzz.R'
Repository: CRAN
Repository/R-Forge/Project: openrepgrid
Repository/R-Forge/Revision: 24
Date/Publication: 2011-07-23 13:02:45
Packaged: 2011-07-06 20:42:29 UTC; rforge

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Package MultiPhen updated to version 0.2 with previous version 0.1 dated 2011-07-06

Title: MultiPhen, a package for the genetic association testing of multiple phenotypes
Description: Performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model)
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart and Federico Calboli
Maintainer: Federico Calboli

Diff between MultiPhen versions 0.1 dated 2011-07-06 and 0.2 dated 2011-07-23

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Package MDR updated to version 1.1 with previous version 1.0 dated 2010-12-13

Title: Detect gene-gene interactions using multifactor dimensionality reduction
Description: Performs multifactor dimensionality reduction (MDR) to detect potential gene-gene interactions in case-control studies.
Author: Stacey Winham
Maintainer: Stacey Winham

Diff between MDR versions 1.0 dated 2010-12-13 and 1.1 dated 2011-07-23

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Package MCMCpack updated to version 1.1-1 with previous version 1.0-11 dated 2011-04-26

Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.2. All models return coda mcmc objects that can then be summarized using the coda package. MCMCpack also contains some useful utility functions, including some additional density functions and pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Andrew D. Martin

Diff between MCMCpack versions 1.0-11 dated 2011-04-26 and 1.1-1 dated 2011-07-23

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Package MCMChybridGP updated to version 4.2 with previous version 3.1 dated 2010-09-30

Title: Hybrid Markov chain Monte Carlo using Gaussian Processes
Description: Hybrid Markov chain Monte Carlo (MCMC) to simulate from a multimodal target distribution. A Gaussian process approximation makes this possible when derivatives are unknown. The Package serves to minimize the number of function evaluations in Bayesian calibration of computer models using parallel tempering. It allows replacement of the true target distribution in high temperature chains, or complete replacement of the target. Methods used are described in, "Efficient MCMC schemes for Bayesian calibration of computer models", Fielding, Mark, Nott, David J. and Liong Shie-Yui, Technometrics (2010). The authors gratefully acknowledge the support & contributions of the Singapore-Delft Water Alliance (SDWA). The research presented in this work was carried out as part of the SDWA's Multi-Objective Multi-Reservoir Management research programme (R-264-001-272).
Author: Mark J. Fielding
Maintainer: Mark J. Fielding

Diff between MCMChybridGP versions 3.1 dated 2010-09-30 and 4.2 dated 2011-07-23

 DESCRIPTION               |   10 +++++-----
 R/MCMChybridGP-internal.R |   11 ++++++++---
 R/hybrid.sample.R         |    2 +-
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Package LaplacesDemon updated to version 11.07.15 with previous version 11.07.05 dated 2011-07-05

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

Diff between LaplacesDemon versions 11.07.05 dated 2011-07-05 and 11.07.15 dated 2011-07-23

 CHANGELOG                       |   18 
 DESCRIPTION                     |    8 
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Package LMERConvenienceFunctions updated to version 1.6.3 with previous version 1.6.2 dated 2011-06-29

Title: A suite of functions to back-fit fixed effects and forward-fit random effects, as well as other miscellaneous functions.
Description: Functions to back-fit fixed effects (on F or t values and, potentially, log-likelihood ratio testing) and to forward-fit random effects (using log-likelihood ratio testing). Note that the back- and forward-fitting of generalized linear mixed-effects regression (\code{glmer}s) models is not yet supported. The package also includes a function to compute ANOVAs with upper- and lower-bound p-values (anti-conservative and conservative, respectively), a function to graph model criticism plots, functions to trim data on model residuals or on a response variable (per subject), a function to perform posthoc analyses, a function to generate (dynamic) 3d plots of (i) predicted values of an LMER model for interactions between two numeric variables,(ii) the raw data as a function of two numeric variable, and (iii) kernel density estimates (densities) of two numeric variables.
Author: Antoine Tremblay
Maintainer: Antoine Tremblay, IWK Health Center

Diff between LMERConvenienceFunctions versions 1.6.2 dated 2011-06-29 and 1.6.3 dated 2011-07-23

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Package FrF2 updated to version 1.2-4 with previous version 1.2-2 dated 2011-02-07

Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional Factorial designs. Furthermore, analysis tools for Fractional Factorial designs with 2-level factors are offered (main effects and interaction plots for all factors simultaneously, cube plot for looking at the simultaneous effects of three factors, full or half normal plot, alias structure in a more readable format than with the built-in function alias). The package is currently subject to intensive development. While much of the intended functionality is already available, some changes and improvements are still to be expected. Suggestions are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping

Diff between FrF2 versions 1.2-2 dated 2011-02-07 and 1.2-4 dated 2011-07-23

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Package DoE.wrapper updated to version 0.8-3 with previous version 0.8-2 dated 2011-01-31

Title: Wrapper package for design of experiments functionality
Description: This package creates various kinds of designs for (industrial) experiments. It uses, and sometimes enhances, design generation routines from other packages. Initially, response surface designs from package rsm and latin hypercube samples from package lhs have been implemented.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping

Diff between DoE.wrapper versions 0.8-2 dated 2011-01-31 and 0.8-3 dated 2011-07-23

 DESCRIPTION       |   10 ++---
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Package BAMD updated to version 3.5 with previous version 3.4 dated 2011-02-19

Title: Bayesian Association Model for Genomic Data with Missing Covariates
Description: This package fits a linear mixed model where the covariates for the random effects have missing values.
Author: Gopal, V. and Li, Z. and Casella, G.
Maintainer: Gopal, V.

Diff between BAMD versions 3.4 dated 2011-02-19 and 3.5 dated 2011-07-23

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New package CLSOCP with initial version 1.0
Package: CLSOCP
Type: Package
Title: A smoothing Newton method SOCP solver
Version: 1.0
Date: 2010-11-05
Author: Jason Rudy
Maintainer: Jason Rudy
Description: This package provides and implementation of a one step smoothing newton method for the solution of second order cone programming problems, originally described by Xiaoni Chi and Sanyang Liu.
Depends: Matrix
License: GPL-3
LazyLoad: yes
Packaged: 2011-07-17 22:05:03 UTC; jasonrudy
Repository: CRAN
Date/Publication: 2011-07-23 13:01:34

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