Mon, 30 Nov 2009

Package testthat updated to version 0.1.1 with previous version 0.1 dated 2009-11-17

Author: Hadley Wickham
Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun, flexible and easy to set up.

Diff between testthat versions 0.1 dated 2009-11-17 and 0.1.1 dated 2009-11-30

 DESCRIPTION     |   11 ++++++-----
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 2 files changed, 9 insertions(+), 6 deletions(-)

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New package phyloclim with initial version 0.0.1
Package: phyloclim
Type: Package
Title: Integrating phylogenetics and climatic niche modelling
Version: 0.0.1
Date: 2009-11-27
Author: Christoph Heibl
Maintainer: Christoph Heibl
Depends: ape, adehabitat
Description: This package implements some recently developed methods in phyloclimatic modeling.
License: GPL (>= 2)
Packaged: 2009-11-30 18:39:21 UTC; Stoffi
Repository: CRAN
Date/Publication: 2009-11-30 20:26:59

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Package benchden updated to version 1.0.3 with previous version 1.0.2 dated 2009-09-28

Author: Thoralf Mildenberger, Henrike Weinert, Sebastian Tiemeyer
Title: 28 benchmark densities from Berlinet/Devroye (1994)
Description: Full implementation of the 28 distributions introduced as benchmarks for nonparametric density estimation by Berlinet and Devroye (1994). Includes densities, cdfs, quantile functions and generators for samples as well as additional information on features of the densities. Also contains the 4 histogram densities used in Rozenholc/Mildenberger/Gather (2009).

Diff between benchden versions 1.0.2 dated 2009-09-28 and 1.0.3 dated 2009-11-30

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Package CHNOSZ updated to version 0.9 with previous version 0.8 dated 2009-04-23

Author: Jeffrey M. Dick
Title: Chemical Thermodynamics and Activity Diagrams
Description: Calculation of the standard molal thermodynamic properties and chemical affinities of reactions between and among minerals, inorganic, organic, and/or biomolecular aqueous and crystalline species. Incorporation of an extensive database of thermodynamic properties of species and algorithms for computing the standard thermodynamic properties of neutral and ionized proteins from amino acid group contributions. Generation of chemical speciation and predominance diagrams for stable and metastable equilibrium in open systems as a function of temperature, pressure, and chemical activities or fugacities of basis species.

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Package hash updated to version 1.10.0 with previous version 1.0.3 dated 2009-11-05

Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor.

Diff between hash versions 1.0.3 dated 2009-11-05 and 1.10.0 dated 2009-11-30

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Package RScaLAPACK updated to version 0.6.1 with previous version 0.5.1 dated 2005-09-03

Author: Nagiza F. Samatova , Srikanth Yoginath , David Bauer and Guruprasad Kora
Title: A seamless interface to perform parallel computation on linear algebra problems using the ScaLAPACK library.
Description: An R add-on package capable of carrying out parallel computation through a single function call from the R environment. It uses the high-performance ScaLAPACK library for the linear algebra computations.

Diff between RScaLAPACK versions 0.5.1 dated 2005-09-03 and 0.6.1 dated 2009-11-30

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Package sandwich updated to version 2.2-3 with previous version 2.2-2 dated 2009-11-17

Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series and longitudinal data.

Diff between sandwich versions 2.2-2 dated 2009-11-17 and 2.2-3 dated 2009-11-30

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Package hmm.discnp updated to version 0.1-1 with previous version 0.1-0 dated 2009-09-28

Author: Rolf Turner and Limin Liu.
Title: Hidden Markov models with discrete non-parametric observation distributions.
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. Simulates data from such models. Finds most probable underlying hidden states and most probable sequences of such states.

Diff between hmm.discnp versions 0.1-0 dated 2009-09-28 and 0.1-1 dated 2009-11-30

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New package crmn with initial version 0.0.7
Package: crmn
Version: 0.0.7
Date: 2008-05-08
Author: Henning Redestig
Maintainer: Henning Redestig
Title: CCMN and other noRMalizatioN methods for metabolomics data
Depends: pcaMethods (>= 1.20.2), Biobase, pls, methods
Description: Implements the Cross-contribution Compensating Multiple standard Normalization (CCMN) method and other normalization algorithms.
License: GPL (>= 3)
Collate: 'classes.R' 'crmn-package.R' 'misc.R' 'norm.R' 'generic.R'
Packaged: 2009-11-30 03:58:19 UTC; henning
Repository: CRAN
Date/Publication: 2009-11-30 14:27:26

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Package RSEIS updated to version 2.3-1 with previous version 2.2-0 dated 2009-10-15

Author: Jonathan M. Lees
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to analyze seismic data, via, spectrum analysis, wavelet transforms, particle motion, hodograms.

Diff between RSEIS versions 2.2-0 dated 2009-10-15 and 2.3-1 dated 2009-11-30

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Package FD updated to version 1.0-5 with previous version 1.0-1 dated 2009-10-26

Author: Etienne Laliberté, Bill Shipley
Title: Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology
Description: FD is a package to compute different multidimensional FD indices. It implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. It also contains other useful tools for functional ecology.

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Package BiodiversityR updated to version 1.4.2 with previous version 1.4 dated 2009-10-23

Author: Roeland Kindt
Title: GUI for biodiversity and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website.

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Sun, 29 Nov 2009

Package robCompositions updated to version 1.3.2 with previous version 1.2.2 dated 2009-05-08

Author: Matthias Templ, Karel Hron, Peter Filzmoser
Title: Robust Estimation for Compositional Data.
Description: The package includes methods for imputation of compositional data including robust methods, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (alr, clr, ilr, and their inverse transformations).

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Package VIM updated to version 1.3.2 with previous version 1.3 dated 2009-04-19

Author: Matthias Templ, Andreas Alfons
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.

Diff between VIM versions 1.3 dated 2009-04-19 and 1.3.2 dated 2009-11-29

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Package RWeka updated to version 0.3-24 with previous version 0.3-23 dated 2009-10-30

Author: Kurt Hornik, with contributions from Christian Buchta, Torsten Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Both the R interface and Weka itself are contained in the RWeka package. For more information on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

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Package sdcMicro updated to version 2.6.3 with previous version 2.6.2 dated 2009-10-22

Author: Matthias Templ
Title: Statistical Disclosure Control methods for the generation of public- and scientific-use files.
Description: Data from statistical agencies and other institutions are mostly confidential. This package can be used for the generation of save (micro)data, i.e. for the generation of public- and scientific-use files. The package includes also a graphical user interface.

Diff between sdcMicro versions 2.6.2 dated 2009-10-22 and 2.6.3 dated 2009-11-29

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New package symbols with initial version 1.1
Package: symbols
Type: Package
Title: Symbol plots
Version: 1.1
Date: 2009-11-28
Author: Jaroslav Myslivec
Maintainer: Jaroslav Myslivec
Depends: R (>= 2.9.1), shape
Description: Package that implements various symbol plots (bars, profiles, stars, Chernoff faces, color icons, stick figures).
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-28 13:06:01 UTC; Myslivec
Repository: CRAN
Date/Publication: 2009-11-29 17:23:35

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Package rattle updated to version 2.5.7 with previous version 2.5.6 dated 2009-11-24

Author: Graham Williams
Title: A graphical user interface for data mining in R using GTK
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 and so available to the user as a script file or as an aide to the user to interact directly with 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.

Diff between rattle versions 2.5.6 dated 2009-11-24 and 2.5.7 dated 2009-11-29

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Package lmomRFA updated to version 2.2 with previous version 2.1 dated 2009-07-18

Author: J. R. M. Hosking
Title: Regional frequency analysis using L-moments
Description: Functions for regional frequency analysis using the methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis: an approach based on L-moments".

Diff between lmomRFA versions 2.1 dated 2009-07-18 and 2.2 dated 2009-11-29

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Package lmom updated to version 1.5 with previous version 1.4 dated 2009-07-18

Author: J. R. M. Hosking
Title: L-moments
Description: Functions related to L-moments: computation of L-moments of distributions and data samples; parameter estimation; L-moment ratio diagram; plot vs. quantiles of an extreme-value distribution.

Diff between lmom versions 1.4 dated 2009-07-18 and 1.5 dated 2009-11-29

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New package formula.tools with initial version 0.14.1
Package: formula.tools
Type: Package
Title: Tools for working with formulas, expressions, calls and other R objects
Version: 0.14.1
Date: 2009-11-28
Author: Christopher Brown
Maintainer: Christopher Brown
Description: This package provides a number of useful utilities for working with formulas, expressions, calls, names, symbols and other R objects. This packagewas designed to greatly facilitate symbolic manupulation using native R objects.
Depends: R (>= 2.9.0), hash (>= 0.40), methods
License: LGPL (>= 2)
URL: http://www.opendatagroup.com, http://blog.opendatagroup.com
LazyLoad: yes
LazyData: yes
Packaged: 2009-11-28 21:36:00 UTC; cbrown
Repository: CRAN
Date/Publication: 2009-11-29 17:23:14

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Package ascii updated to version 0.4-2 with previous version 0.4-1 dated 2009-11-26

Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or org syntax. Package comes with a set of drivers for Sweave.

Diff between ascii versions 0.4-1 dated 2009-11-26 and 0.4-2 dated 2009-11-29

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Package WINRPACK updated to version 1.1-0 with previous version 1.0-9 dated 2009-09-28

Author: Jonathan M. Lees
Title: Read in WIN format data
Description: Reads in WIN pickfile and waveform file, prepares data for RSEIS

Diff between WINRPACK versions 1.0-9 dated 2009-09-28 and 1.1-0 dated 2009-11-29

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Package MCMCpack updated to version 1.0-5 with previous version 1.0-4 dated 2009-09-08

Author: Andrew D. Martin , Kevin M. Quinn , Jong Hee Park
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.

Diff between MCMCpack versions 1.0-4 dated 2009-09-08 and 1.0-5 dated 2009-11-29

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Package DEoptim updated to version 2.0-3 with previous version 2.0-1 dated 2009-10-07

Author: David Ardia and Katharine Mullen
Title: Global optimization by differential evolution
Description: This package provides the DEoptim function which performs global optimization by differential evolution.

Diff between DEoptim versions 2.0-1 dated 2009-10-07 and 2.0-3 dated 2009-11-29

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New package Cprob with initial version 1.0
Package: Cprob
Title: Conditional probability function of a competing event
Version: 1.0
Author: Arthur Allignol
Description: Estimates the conditional probability function of a competing event, and fits, using the temporal process regression or the pseudo-value approach, a proportional-odds model to the conditional probability function
Maintainer: Arthur Allignol
Depends: prodlim, tpr, lattice, geepack
License: GPL (>= 2)
Packaged: 2009-11-28 21:17:20 UTC; arthur
Repository: CRAN
Date/Publication: 2009-11-29 17:22:48

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Fri, 27 Nov 2009

Package plsdof updated to version 0.1-1 with previous version 0.1 dated 2009-11-16

Author: Nicole Kraemer, Mikio L. Braun
Title: Degrees of Freedom and Confidence Intervals for Partial Least Squares Regression
Description: The plsdof package provides Degrees of Freedom estimates for Kernel Partial Least Squares Regression and its kernel extension. The package also provides model selection based on various information criteria (aic, bic, gmdl) and based on cross-validation. For linear Partial Least Squares, the package computes the approximate distribution of the regression coefficients. This allows the construction of confidence intervals and tests.

Diff between plsdof versions 0.1 dated 2009-11-16 and 0.1-1 dated 2009-11-27

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Package phangorn updated to version 0.99-4 with previous version 0.99-3 dated 2009-10-30

Author: Klaus Schliep
Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)

Diff between phangorn versions 0.99-3 dated 2009-10-30 and 0.99-4 dated 2009-11-27

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Package DDHFm updated to version 1.0-3 with previous version 1.0-2.1 dated 2009-02-23

Author: Efthimios S. Motakis, Guy P. Nason, Piotr Fryzlewicz
Title: Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays)
Description: The package contains the normalizing and variance stabilizing Data-Driven Haar-Fisz algorithm. Also contains related algorithms for simulating from certain microarray gene intensity models and evaluation of certain transformations.

Diff between DDHFm versions 1.0-2.1 dated 2009-02-23 and 1.0-3 dated 2009-11-27

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Package setRNG updated to version 2009.11-1 with previous version 2008.3-1 dated 2008-03-21

Author: Paul Gilbert
Title: Set (Normal) Random Number Generator and Seed
Description: SetRNG provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.

Diff between setRNG versions 2008.3-1 dated 2008-03-21 and 2009.11-1 dated 2009-11-27

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Package mixer updated to version 1.1 with previous version 1.0 dated 2009-11-19

Author: Christophe Ambroise, Gilles Grasseau, Mark Hoebeke, Pierre Latouche, Vincent Miele, Franck Picard
Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of networks using MIXtures of Erdos-Renyi random graphs

Diff between mixer versions 1.0 dated 2009-11-19 and 1.1 dated 2009-11-27

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Package lpSolveAPI updated to version 5.5.0.15-1 with previous version 5.5.0.15 dated 2009-09-28

Author: lp_solve , Kjell Konis .
Title: Interface to lp_solve 5.5.0.15
Description: The lpSolveAPI package provides an R interface to the lp_solve library API - lp_solve is a Mixed Integer Linear Programming (MILP) solver with support for pure linear, (mixed) integer/binary, semi-continuous and special ordered sets (SOS) models.

Diff between lpSolveAPI versions 5.5.0.15 dated 2009-09-28 and 5.5.0.15-1 dated 2009-11-27

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Package DoE.base updated to version 0.9-10 with previous version 0.9-8 dated 2009-11-26

Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.

Diff between DoE.base versions 0.9-8 dated 2009-11-26 and 0.9-10 dated 2009-11-27

 DESCRIPTION         |    8 ++++----
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Thu, 26 Nov 2009

Package tnet updated to version 0.1.3 with previous version 0.1.2 dated 2009-09-18

Author: Tore Opsahl
Title: tnet: Software for Analysis of Weighted, Two-mode, and Longitudinal networks
Description: R package to analyse weighted, two-mode, and longitudinal networks.

Diff between tnet versions 0.1.2 dated 2009-09-18 and 0.1.3 dated 2009-11-26

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Package spdep updated to version 0.4-54 with previous version 0.4-52 dated 2009-11-05

Author: Roger Bivand , with contributions by Luc Anselin, Renato Assunção, Olaf Berke, Andrew Bernat, Marilia Carvalho, Yongwan Chun, Bjarke Christensen, Carsten Dormann, Stéphane Dray, Rein Halbersma, Elias Krainski, Nicholas Lewin-Koh, Hongfei Li, Jielai Ma, Giovanni Millo, Werner Mueller, Hisaji Ono, Pedro Peres-Neto, Markus Reder, Michael Tiefelsdorf, and Danlin Yu.
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tesselations, for summarising these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.

Diff between spdep versions 0.4-52 dated 2009-11-05 and 0.4-54 dated 2009-11-26

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Package pARccs updated to version 0.2-1 with previous version 0.1-1 dated 2008-10-15

Author: Christiane Raemsch
Title: Estimation of attributable and partial attributable risks (AR and PAR) and visualization of attributable risks from case-control data
Description: Functions to estimate (partial) attributable risks from case-control data with corresponding percentile or BCa confidence intervals; Visualization of attributable riks

Diff between pARccs versions 0.1-1 dated 2008-10-15 and 0.2-1 dated 2009-11-26

 DESCRIPTION       |   29 +++---
 NAMESPACE         |    5 -
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Package nor1mix updated to version 1.1-1 with previous version 1.0-7 dated 2007-06-12

Author: Martin Mächler
Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities, see ?MarronWand.

Diff between nor1mix versions 1.0-7 dated 2007-06-12 and 1.1-1 dated 2009-11-26

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Package log10 updated to version 0.1.0-01 with previous version 0.0.3-05 dated 2009-11-22

Author: Timothee Poisot
Title: Decimal log plotting in two and three dimensions
Description: Provides a range of function for 10-log plotting

Diff between log10 versions 0.0.3-05 dated 2009-11-22 and 0.1.0-01 dated 2009-11-26

 DESCRIPTION    |   10 +++++-----
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Package FrF2 updated to version 1.0-2 with previous version 1.0-1 dated 2009-11-18

Author: Ulrike Groemping
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.

Diff between FrF2 versions 1.0-1 dated 2009-11-18 and 1.0-2 dated 2009-11-26

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Package FactoClass updated to version 1.0.3 with previous version 1.0.1 dated 2009-07-21

Author: Campo Elias Pardo and Pedro Cesar del Campo , with the contributions from Camilo Jose Torres , Ivan Diaz , Mauricio Sadinle .
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial analysis and cluster methods.

Diff between FactoClass versions 1.0.1 dated 2009-07-21 and 1.0.3 dated 2009-11-26

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Package DoE.base updated to version 0.9-8 with previous version 0.9-7 dated 2009-11-05

Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.

Diff between DoE.base versions 0.9-7 dated 2009-11-05 and 0.9-8 dated 2009-11-26

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Package copas updated to version 0.6-3 with previous version 0.6-2 dated 2009-04-15

Author: James Carpenter , Guido Schwarzer
Title: Statistical methods to model and adjust for bias in meta-analysis
Description: Copas selection model.

Diff between copas versions 0.6-2 dated 2009-04-15 and 0.6-3 dated 2009-11-26

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Package NMF updated to version 0.2.2 with previous version 0.2 dated 2009-11-23

Author: Renaud Gaujoux
Title: Framework for Nonnegative Matrix Factorization (NMF) algorithms.
Description: This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test and develop new algorithms.

Diff between NMF versions 0.2 dated 2009-11-23 and 0.2.2 dated 2009-11-26

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Package timereg updated to version 1.2-7 with previous version 1.2-5 dated 2009-07-31

Author: Thomas Scheike with contributions from Torben Martinussen and Jeremy Silver
Title: timereg package for Flexible regression models for survival data.
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparmetric proportional odds model, cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling.

Diff between timereg versions 1.2-5 dated 2009-07-31 and 1.2-7 dated 2009-11-26

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Package msm updated to version 0.9.5 with previous version 0.9.4 dated 2009-11-13

Author: Christopher Jackson
Title: Multi-state Markov and hidden Markov models in continuous time
Description: Functions for fitting general continuous-time Markov and hidden Markov multi-state models to longitudinal data. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates. A variety of observation schemes are supported, including processes observed at arbitrary times, completely-observed processes, and censored states.

Diff between msm versions 0.9.4 dated 2009-11-13 and 0.9.5 dated 2009-11-26

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Package fossil updated to version 0.2.2 with previous version 0.2.1 dated 2009-04-14

Author: Matthew Vavrek
Title: Palaeoecological and Palaeogeographical Analysis Tools
Description: A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.

Diff between fossil versions 0.2.1 dated 2009-04-14 and 0.2.2 dated 2009-11-26

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Package ascii updated to version 0.4-1 with previous version 0.4 dated 2009-11-25

Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or org syntax. Package comes with a set of drivers for Sweave.

Diff between ascii versions 0.4 dated 2009-11-25 and 0.4-1 dated 2009-11-26

 DESCRIPTION    |    6 +++---
 NAMESPACE      |    2 ++
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New package OligoSpecificitySystem with initial version 1.0
Package: OligoSpecificitySystem
Title: Oligo Specificity System
Version: 1.0
Date: 2009-10-15
Author: Rory Michelland ,Laurent Cauquil
Maintainer: Laurent Cauquil
Description: Calculate the theorical specificity of a system of multiple primers used for PCR, qPCR primers or degenerated primer design
Depends: tcltk,tkrplot
License: GPL-2
Packaged: 2009-11-25 11:06:27 UTC; Rory
Repository: CRAN
Date/Publication: 2009-11-26 08:03:07

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Package GWAF updated to version 1.2 with previous version 1.1 dated 2009-09-25

Author: Ming-Huei Chen and Qiong Yang
Title: Genome-Wide Association analyses with Family data
Description: Functions to test genetic associations between SNPs and a continuous/dichotomous trait using family data, and to make genome-wide p-value plot and QQ plot.

Diff between GWAF versions 1.1 dated 2009-09-25 and 1.2 dated 2009-11-26

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Wed, 25 Nov 2009

New package twopartqtl with initial version 1.0
Package: twopartqtl
Type: Package
Title: QTL Mapping for Point-mass Mixtures
Version: 1.0
Date: 2009-07-22
Author: Sandra L. Taylor
Maintainer: Sandra L. Taylor
Description: Composite interval mapping to identify QTLs in experimental crosses with phenotypes distributed as point-mass mixtures
Depends: qtl
License: GPL (>= 2)
LazyLoad: yes
Packaged: Tue Nov 24 08:45:32 2009; sltaylor
Repository: CRAN
Date/Publication: 2009-11-25 08:29:47

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Package nnDiag updated to version 0.0-4 with previous version 0.0-3 dated 2009-11-17

Author: Brian Walters , Andrew O. Finley , Zhen Zhang
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN classifications.

Diff between nnDiag versions 0.0-3 dated 2009-11-17 and 0.0-4 dated 2009-11-25

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Package hapassoc updated to version 1.2-3 with previous version 1.2-2 dated 2008-10-14

Author: K. Burkett , B. McNeney , J. Graham , with code for case-control data contributed by Zhijian Chen
Title: Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm
Description: The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.

Diff between hapassoc versions 1.2-2 dated 2008-10-14 and 1.2-3 dated 2009-11-25

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Package bayesGARCH updated to version 1-00.05 with previous version 1-00.04 dated 2009-05-11

Author: David Ardia
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
Description: This package provides the bayesGARCH function which performs the Bayesian estimation of the GARCH(1,1) model with Student's t innovations.

Diff between bayesGARCH versions 1-00.04 dated 2009-05-11 and 1-00.05 dated 2009-11-25

 DESCRIPTION       |    8 ++++----
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Package ascii updated to version 0.4 with previous version 0.3.2 dated 2009-10-28

Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or org syntax. Package comes with a set of drivers for Sweave.

Diff between ascii versions 0.3.2 dated 2009-10-28 and 0.4 dated 2009-11-25

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Package accuracy updated to version 1.34 with previous version 1.33 dated 2009-10-30

Author: Micah Altman, Jeff Gill, Michael P. McDonald
Title: Tools for testing and improving accuracy of statistical results.
Description: This is a suite of tools designed to test and improve the accuracy of statistical computation, including: Summarization of the sensitivity of linear and non-linear models (lm, glm, mle, nls) to measurement and numerical error; Sensitivity analysis of dozens of models as run through Zelig; A generalized cholesky method for correcting non-invertable Hessians; Tests for the global optimality of non-linear regression and maximum likelihood results; Tools for obtaining true random numbers using entropy collected from the system and/or entropy servers on the internet; A method for converting floating point numbers to normalized fractions; Benchmark data for checking the accuracy of basic distribution functions.

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More information about accuracy at CRAN
Permanent link

Package PBSmodelling updated to version 2.51.168 with previous version 2.50.162 dated 2009-10-20

Author: Jon T. Schnute , Alex Couture-Beil , Rowan Haigh , and Anisa Egeli
Title: GUI Tools Made Easy: Interact with Models, Explore Data, Give Dynamic Presentations
Description: PBS Modelling provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface (GUI). Although it depends heavily on the R interface to the Tcl/Tk package, a user does not need to know Tcl/Tk. The package contains examples that illustrate models built with other R packages, including PBSmapping, deSolve, PBSddesolve, and BRugs. It also serves as a convenient prototype for building new R packages, along with instructions and batch files to facilitate that process. The R directory '.../library/PBSmodelling/doc' includes a complete user guide PBSmodelling-UG.pdf. To use this package effectively, please consult the guide.

Diff between PBSmodelling versions 2.50.162 dated 2009-10-20 and 2.51.168 dated 2009-11-25

 DESCRIPTION                      |   12 ++++----
 NAMESPACE                        |    1 
 R/presentTalk.r                  |    5 ++-
 R/supportFuns.r                  |   56 ++++++++++++++++++++++++++++-----------
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 inst/doc/ChangeLog.txt           |    6 ++++
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 man/showHelp.Rd                  |   24 +++++++++-------
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 12 files changed, 86 insertions(+), 38 deletions(-)

More information about PBSmodelling at CRAN
Permanent link

Package PASWR updated to version 1.1 with previous version 1.0 dated 2008-02-12

Author: Alan T. Arnholt
Title: PROBABILITY and STATISTICS WITH R
Description: Data and functions for the book PROBABILITY and STATISTICS WITH R.

Diff between PASWR versions 1.0 dated 2008-02-12 and 1.1 dated 2009-11-25

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Permanent link

New package PBSadmb with initial version 0.60.43
Package: PBSadmb
Version: 0.60.43
Date: 2009-11-20
Title: PBS ADMB
Author: Jon T. Schnute, Rowan Haigh
Maintainer: Jon T. Schnute
Depends: R (>= 2.7.0), PBSmodelling (>= 2.50)
Description: R Support for ADMB (Automatic Differentiation Model Builder)
License: GPL (>= 2)
Packaged: 2009-11-21 03:33:50 UTC; Fish
Repository: CRAN
Date/Publication: 2009-11-25 08:29:21

More information about PBSadmb at CRAN
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New package LogitNet with initial version 0.1-1
Package: LogitNet
Version: 0.1-1
Date: 2009-11-20
Title: Infer network based on binary arrays using regularized logistic regression
Author: Pei Wang , Dennis Chao , Li Hsu
Maintainer: Pei Wang
Description: LogitNet is developed for inferring network of binary variables under the high-dimension-low-sample-size setting
License: GPL (>= 2)
Packaged: 2009-11-25 03:43:04 UTC; pwang
Repository: CRAN
Date/Publication: 2009-11-25 08:38:21

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Package DAAG updated to version 1.01 with previous version 1.00 dated 2009-08-23

Author: John Maindonald and W. John Braun
Title: Data Analysis And Graphics data and functions
Description: various data sets used in examples and exercises in the book Maindonald, J.H. and Braun, W.J. (2003, 2007) "Data Analysis and Graphics Using R".

Diff between DAAG versions 1.00 dated 2009-08-23 and 1.01 dated 2009-11-25

 DESCRIPTION    |    8 ++++----
 INDEX          |   14 +++++++-------
 R/pause.R      |    3 +--
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 4 files changed, 13 insertions(+), 13 deletions(-)

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Package AquaEnv updated to version 0.8-1 with previous version 0.8 dated 2009-11-18

Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Title: AquaEnv - an integrated development toolbox for aquatic chemical model generation
Description: AquaEnv is an integrated development toolbox for aquatic chemical model generation focused on (ocean) acidification and CO2 air-water exchange. It contains all elements necessary to model the pH, the related CO2 air-water exchange, as well as aquatic acid-base chemistry in general for an arbitrary marine, estuarine or freshwater system. Also chemical batches can be modelled. Next to the routines necessary to calculate desired information, AquaEnv also contains a suite of tools to visualize this information. Furthermore, AquaEnv can not only be used to build dynamic models of aquatic systems, but it can also serve as a simple desktop tool for the experimental aquatic chemist to generate and visualize all possible derived information from a set of measurements with one single easy to use R function. Additionally, the sensitivity of the system to variations in the input variables can be visualized.

Diff between AquaEnv versions 0.8 dated 2009-11-18 and 0.8-1 dated 2009-11-25

 DESCRIPTION                               |   10 
 R/aquaenv_private_DSApHfunctions.R        |  292 
 inst/doc/AquaEnv-ConstantsAndFormulae.pdf | 5425 +++++-----
 inst/doc/AquaEnv-PrivateFunctions.pdf     |binary
 inst/doc/AquaEnv.pdf                      |14858 ++++++++++++++----------------
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 6 files changed, 13152 insertions(+), 13287 deletions(-)

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Tue, 24 Nov 2009

Package stab updated to version 0.0.6 with previous version 0.0.5 dated 2008-11-04

Author: Hsin-ya Lee , Yung-jin Lee
Title: data analysis of drug stability
Description: A menu-driven package for data analysis of drug stability based on ICH guideline(such as estimation of shelf-life from a 3-batch profile.)

Diff between stab versions 0.0.5 dated 2008-11-04 and 0.0.6 dated 2009-11-24

 DESCRIPTION            |   27 ++++++++++++++++-----------
 R/MultipleAnalyze.r    |    4 ++--
 R/stabilitymenu.r      |    2 +-
 R/zzz.R                |    2 +-
 man/MultipleAnalyze.rd |    2 +-
 5 files changed, 21 insertions(+), 16 deletions(-)

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Package rattle updated to version 2.5.6 with previous version 2.5.3 dated 2009-11-06

Author: Graham Williams
Title: A graphical user interface for data mining in R using GTK
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 and so available to the user as a script file or as an aide to the user to interact directly with 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.

Diff between rattle versions 2.5.3 dated 2009-11-06 and 2.5.6 dated 2009-11-24

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Package bayescount updated to version 0.9.9-1 with previous version 0.9.0-7 dated 2009-01-08

Author: Matthew Denwood (funded as part of the DEFRA VTRI project 0101).
Title: Power calculations and Bayesian analysis of count distributions and FECRT data using MCMC
Description: A set of functions to allow analysis of count data (such as faecal egg count data) using Bayesian MCMC methods. Returns information on the possible values for mean count, coefficient of variation and zero inflation (true prevalence) present in the data. A complete faecal egg count reduction test (FECRT) model is implemented, which returns inference on the true efficacy of the drug from the pre and post treatment data provided, using non-parametric bootstrapping as well as using Bayesian MCMC. Functions to perform power analyses for faecal egg counts (including FECRT) are also provided. Requires Just Another Gibbs Sampler (JAGS) for most functions (except power analysis calculations), see: http://www-fis.iarc.fr/~martyn/software/jags/.

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Package vrmlgen updated to version 1.3 with previous version 1.2 dated 2009-11-12

Author: Enrico Glaab
Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes, parametric functions and height maps in web-formats like the Virtual Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

Diff between vrmlgen versions 1.2 dated 2009-11-12 and 1.3 dated 2009-11-24

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Package vegdata updated to version 0.1.1 with previous version 0.1 dated 2009-11-11

Author: Florian Jansen
Title: Functions to use vegetation databases (Turboveg) for vegetation analyses in R
Description: Handling of vegetation data sets from Turboveg Databases. Taxonomic valuation for German Taxonomical Standard List.

Diff between vegdata versions 0.1 dated 2009-11-11 and 0.1.1 dated 2009-11-24

 vegdata-0.1.1/vegdata/DESCRIPTION                             |    6 
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 vegdata-0.1.1/vegdata/inst/CITATION                           |    4 
 vegdata-0.1.1/vegdata/inst/ChangeLog                          |    3 
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 vegdata-0.1.1/vegdata/inst/doc/vegdata.pdf                    |26955 +++++-----
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Package pedigree updated to version 1.2 with previous version 1.1 dated 2009-02-24

Author: Albart Coster
Title: Pedigree functions
Description: Pedigree related functions

Diff between pedigree versions 1.1 dated 2009-02-24 and 1.2 dated 2009-11-24

 pedigree-1.1/pedigree/Read-and-delete-me |only
 pedigree-1.2/pedigree/DESCRIPTION        |   10 +-
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 pedigree-1.2/pedigree/src/Pedigree.h     |   11 +-
 9 files changed, 160 insertions(+), 46 deletions(-)

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Package aspace updated to version 2.2 with previous version 1.2 dated 2007-05-08

Author: Randy Bui, Ron N. Buliung, Tarmo K. Remmel
Title: A collection of functions for estimating centrographic statistcs and computational geometries for spatial point patterns
Description: A collection of functions for computing centrographic statistics (e.g., standard distance, standard deviation ellipse, standard deviation box), and minimum convex polygons (MCP) for observations taken at point locations. A tool is also provided for converting geometric objects associated with the centrographic statistics, and MCPs into ESRI Shapefiles. Separate plotting functions have been developed for each measure.

Diff between aspace versions 1.2 dated 2007-05-08 and 2.2 dated 2009-11-24

 DESCRIPTION           |   27 ++--
 NAMESPACE             |    2 
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Package HaploSim updated to version 1.8.1 with previous version 1.8 dated 2009-04-14

Author: Albart Coster, John Bastiaansen
Title: HaploSim
Description: Simulate haplotypes through meioses. Allows specification of population parameters.

Diff between HaploSim versions 1.8 dated 2009-04-14 and 1.8.1 dated 2009-11-24

 DESCRIPTION        |   10 +++++-----
 R/SamplePedigree.R |    2 +-
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 3 files changed, 39 insertions(+), 6 deletions(-)

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Package ChainLadder updated to version 0.1.2-13 with previous version 0.1.2-11 dated 2009-03-28

Author: Markus Gesmann
Title: Mack-, Bootstrap and Munich-chain-ladder methods for insurance claims reserving
Description: The package provides Mack-, Munich-, and Bootstrap chain-ladder methods. These methods are typically used in insurance claims reserving.

Diff between ChainLadder versions 0.1.2-11 dated 2009-03-28 and 0.1.2-13 dated 2009-11-24

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Mon, 23 Nov 2009

Package pbatR updated to version 2.2-0 with previous version 2.1.5 dated 2009-06-18

Author: Thomas Hoffmann , with contributions from Christoph Lange
Title: P2BAT
Description: This package provides data analysis via the pbat program, and an alternative internal implementation of the power calculations via simulation only. For analysis, this package provides a frontend to the PBAT software, automatically reading in the output from the pbat program and displaying the corresponding figure when appropriate (i.e. PBAT-logrank). It includes support for multiple processes and clusters. For analysis, users must download PBAT (developed by Christoph Lange) and accept it's license, available on the PBAT webpage. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.

Diff between pbatR versions 2.1.5 dated 2009-06-18 and 2.2-0 dated 2009-11-23

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Package modTempEff updated to version 1.4 with previous version 1.3 dated 2009-11-22

Author: Vito M. R. Muggeo
Title: Modelling temperature effects using time series data
Description: Fits a Constrained Segmented Distributed Lag regression model to epidemiological time series of mortality, temperature, and other confounders.

Diff between modTempEff versions 1.3 dated 2009-11-22 and 1.4 dated 2009-11-23

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Package minpack.lm updated to version 1.1-4 with previous version 1.1-3 dated 2009-11-23

Author: Timur V. Elzhov, Katharine M. Mullen
Title: R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK
Description: Provides R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm.

Diff between minpack.lm versions 1.1-3 dated 2009-11-23 and 1.1-4 dated 2009-11-23

 DESCRIPTION     |    6 +++---
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Package fbati updated to version 0.7-1 with previous version 0.6.2 dated 2009-03-11

Author: Thomas Hoffmann
Title: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.

Diff between fbati versions 0.6.2 dated 2009-03-11 and 0.7-1 dated 2009-11-23

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Package ecolMod updated to version 1.2.2 with previous version 1.2.1 dated 2009-02-20

Author: Karline Soetaert , Peter MJ Herman
Title: "A practical guide to ecological modelling - using R as a simulation platform"
Description: Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer. All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11. The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter. Solutions to model projects are in the same subdirectories.

Diff between ecolMod versions 1.2.1 dated 2009-02-20 and 1.2.2 dated 2009-11-23

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Package deSolve updated to version 1.5-1 with previous version 1.5 dated 2009-10-16

Author: Karline Soetaert , Thomas Petzoldt , R. Woodrow Setzer
Title: General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE) and differential algebraic equations (DAE)
Description: Functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE) and of differential algebraic equations (DAE). The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.

Diff between deSolve versions 1.5 dated 2009-10-16 and 1.5-1 dated 2009-11-23

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Package automap updated to version 1.0-5 with previous version 1.0-4 dated 2009-11-17

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

Diff between automap versions 1.0-4 dated 2009-11-17 and 1.0-5 dated 2009-11-23

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Package ape updated to version 2.4-1 with previous version 2.4 dated 2009-10-05

Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

Diff between ape versions 2.4 dated 2009-10-05 and 2.4-1 dated 2009-11-23

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New package NMF with initial version 0.2
Package: NMF
Type: Package
Title: Framework for Nonnegative Matrix Factorization (NMF) algorithms.
Version: 0.2
Date: 2009-08-25
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
Description: This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test and develop new algorithms.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.9.2), methods, stats
Imports: Biobase
Suggests: RColorBrewer, fastICA
Collate: utils.R options.R NMF-class.R NMFstd-class.R NMFOffset-class.R NMFns-class.R NMFfit-class.R NMFSet-class.R registry.R NMFStrategy-class.R NMFStrategyFunction-class.R NMFStrategyIterative-class.R fcnnls.R snmf.R lnmf.R ica.R nndsvd.R seed.R nmf.R Bioc-layer.R nmf-package.R
Packaged: 2009-11-23 10:40:16 UTC; renaud
Repository: CRAN
Date/Publication: 2009-11-23 19:19:16

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Package HardyWeinberg updated to version 1.4 with previous version 1.3 dated 2009-03-27

Author: Jan Graffelman
Title: Graphical tests for Hardy-Weinberg equilibrium
Description: Package HardyWeinberg is a package for exploring bi-allelic marker data. It focuses on the graphical representation of the results of tests for Hardy-Weinberg equlibrium in a ternary plot. Routines for several tests for Hardy-Weinberg equilibrium are included in the package.

Diff between HardyWeinberg versions 1.3 dated 2009-03-27 and 1.4 dated 2009-11-23

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Package AlgDesign updated to version 1.1-0 with previous version 1.0-12 dated 2009-09-30

Author: Bob Wheeler
Title: AlgDesign
Description: Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.

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Package emu updated to version 4.2 with previous version 4.1 dated 2009-09-08

Author: Jonathan Harrington and others, IPS LMU Muenchen & IPDS CAU Kiel
Title: Interface to the Emu Speech Database System
Description: Provides an interface to the Emu speech database system and many special purpose functions for display and analysis of speech data.

Diff between emu versions 4.1 dated 2009-09-08 and 4.2 dated 2009-11-23

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Package TGUITeaching updated to version 0.9.3 with previous version 0.9.2 dated 2009-11-19

Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Title: Teaching GUI - prototype
Description: Trainings-GUI

Diff between TGUITeaching versions 0.9.2 dated 2009-11-19 and 0.9.3 dated 2009-11-23

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Package TGUICore updated to version 0.9.3 with previous version 0.9.2 dated 2009-11-19

Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Title: Teaching GUI - Core functionality
Description: Trainings-GUI

Diff between TGUICore versions 0.9.2 dated 2009-11-19 and 0.9.3 dated 2009-11-23

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Package MLCM updated to version 0.0-7 with previous version 0.0-6 dated 2009-10-05

Author: Kenneth Knoblauch and Laurence T. Maloney
Title: Maximum Likelihood Conjoint Measurement
Description: Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along 2 or more dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact.

Diff between MLCM versions 0.0-6 dated 2009-10-05 and 0.0-7 dated 2009-11-23

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Package zoo updated to version 1.6-2 with previous version 1.6-1 dated 2009-11-19

Author: Achim Zeileis, Gabor Grothendieck
Title: 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.

Diff between zoo versions 1.6-1 dated 2009-11-19 and 1.6-2 dated 2009-11-23

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Package xterm256 updated to version 0.1-2 with previous version 0.0 dated 2009-04-20

Author: Romain Francois
Title: Support for xterm256 escape sequences
Description: Support for xterm256 escape sequences, enabling R functions to take advantage of foreground color, background color, in capable terminals

Diff between xterm256 versions 0.0 dated 2009-04-20 and 0.1-2 dated 2009-11-23

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Package oosp updated to version 0.2.3 with previous version 0.2.2 dated 2009-11-22

Author: CHARLOTTE MAIA
Title: Object Oriented Statistical Programming
Description: A platform for, and collection of tools for, object oriented statistical programming in R.

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Package minpack.lm updated to version 1.1-3 with previous version 1.1-1 dated 2008-05-25

Author: Timur V. Elzhov, Katharine M. Mullen
Title: R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK
Description: Provides R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm.

Diff between minpack.lm versions 1.1-1 dated 2008-05-25 and 1.1-3 dated 2009-11-23

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Package MASS updated to version 7.3-4 with previous version 7.3-3 dated 2009-10-28

Author: S original by Venables & Ripley. R port by Brian Ripley , following earlier work by Kurt Hornik and Albrecht Gebhardt.
Title: Main Package of Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition).

Diff between MASS versions 7.3-3 dated 2009-10-28 and 7.3-4 dated 2009-11-23

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Package caGUI updated to version 0.1-2 with previous version 0.1-0 dated 2009-10-04

Author: Angelos Markos
Title: A Tcl/Tk GUI for the functions in the ca package
Description: A Graphical User Interface (GUI) for computation and visualization of simple, multiple and joint correspondence analysis with the ca package.

Diff between caGUI versions 0.1-0 dated 2009-10-04 and 0.1-2 dated 2009-11-23

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Package arm updated to version 1.2-10 with previous version 1.2-9.01 dated 2009-10-01

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

Diff between arm versions 1.2-9.01 dated 2009-10-01 and 1.2-10 dated 2009-11-23

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Sun, 22 Nov 2009

New package someKfwer with initial version 1.0
Package: someKfwer
Type: Package
Title: Controlling the Generalized Familywise Error Rate
Version: 1.0
Date: 2009-10-30
Author: L. Finos and A. Farcomeni
Maintainer: L. Finos
Description: This library collects some procedures controlling the Generalized Familywise Error Rate.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-20 10:55:45 UTC; finos
Repository: CRAN
Date/Publication: 2009-11-22 19:39:38

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Package robustbase updated to version 0.5-0-1 with previous version 0.5-0 dated 2009-11-18

Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov , Andreas Ruckstuhl , Matias Salibian-Barrera , Tobias Verbeke , Martin Maechler
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. The goal is to provide tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.

Diff between robustbase versions 0.5-0 dated 2009-11-18 and 0.5-0-1 dated 2009-11-22

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Package dynamicTreeCut updated to version 1.21 with previous version 1.20 dated 2009-02-05

Author: Peter Langfelder and Bin Zhang , with contributions from Steve Horvath
Title: Methods for detection of clusters in hierarchical clustering dendrograms.
Description: Contains methods for detection of clusters in hierarchical clustering dendrograms.

Diff between dynamicTreeCut versions 1.20 dated 2009-02-05 and 1.21 dated 2009-11-22

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Package tseries updated to version 0.10-22 with previous version 0.10-21 dated 2009-10-04

Author: Compiled by Adrian Trapletti
Title: Time series analysis and computational finance
Description: Package for time series analysis and computational finance

Diff between tseries versions 0.10-21 dated 2009-10-04 and 0.10-22 dated 2009-11-22

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Package mda updated to version 0.3-5 with previous version 0.3-4 dated 2009-01-04

Author: S original by Trevor Hastie & Robert Tibshirani. R port by Friedrich Leisch, Kurt Hornik and Brian D. Ripley.
Title: Mixture and flexible discriminant analysis
Description: Mixture and flexible discriminant analysis, multivariate additive regression splines (MARS), BRUTO, ...

Diff between mda versions 0.3-4 dated 2009-01-04 and 0.3-5 dated 2009-11-22

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Package clue updated to version 0.3-33 with previous version 0.3-32 dated 2009-10-18

Author: Kurt Hornik, with contributions from Walter Boehm
Title: Cluster ensembles
Description: CLUster Ensembles

Diff between clue versions 0.3-32 dated 2009-10-18 and 0.3-33 dated 2009-11-22

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Package bindata updated to version 0.9-17 with previous version 0.9-16 dated 2009-10-08

Author: Friedrich Leisch and Andreas Weingessel and Kurt Hornik
Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.

Diff between bindata versions 0.9-16 dated 2009-10-08 and 0.9-17 dated 2009-11-22

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Package tgp updated to version 2.2-4 with previous version 2.2-3 dated 2009-07-26

Author: Robert B. Gramacy and Matt A. Taddy
Title: Bayesian treed Gaussian process models
Description: Bayesian nonstationary, semiparametric nonlinear regression and design by treed Gaussian processes with jumps to the limiting linear model (LLM). Special cases also implemented include Bayesian linear models, CART, treed linear models, stationary separable and isotropic Gaussian processes. Provides 1-d and 2-d plotting functions (with projection and slice capabilities) and tree drawing, designed for visualization of tgp-class output. Sensitivity analysis and multi-resolution models are supported. Sequential experimental design and adaptive sampling functions are also provided, including ALM, ALC, and expected improvement. The latter supports derivative-free optimization of noisy black-box functions.

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Package sdef updated to version 1.3 with previous version 1.2 dated 2009-09-04

Author: Alberto Cassese, Marta Blangiardo
Title: Synthesizing List of Differentially Expressed Features
Description: The package performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments.

Diff between sdef versions 1.2 dated 2009-09-04 and 1.3 dated 2009-11-22

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Package parser updated to version 0.0-5 with previous version 0.0-3 dated 2009-07-30

Author: Romain Francois
Title: Detailed R source code parser
Description: detailed source code parser, based on the standard R parser but organizing the information differently

Diff between parser versions 0.0-3 dated 2009-07-30 and 0.0-5 dated 2009-11-22

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Package oosp updated to version 0.2.2 with previous version 0.1.0 dated 2009-08-20

Author: CHARLOTTE MAIA
Title: Object Oriented Statistical Programming
Description: A platform for, and collection of tools for, object oriented statistical programming in R.

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Package modTempEff updated to version 1.3 with previous version 1.1 dated 2009-09-20

Author: Vito M. R. Muggeo
Title: Modelling temperature effects using time series data
Description: Fits a Constrained Segmented Distributed Lag regression model to epidemiological time series of mortality, temperature, and other confounders.

Diff between modTempEff versions 1.1 dated 2009-09-20 and 1.3 dated 2009-11-22

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New package ncvreg with initial version 1.0
Package: ncvreg
Title: Regularization paths for SCAD- and MCP-penalized regression models
Version: 1.0
Date: 2009-11-20
Author: Patrick Breheny
Maintainer: Patrick Breheny
Depends:
Description: Efficient algorithms for fitting the regularization path for linear or logistic regression models penalized by MCP or SCAD.
License: GPL-2
Packaged: 2009-11-20 21:09:17 UTC; pbreheny
Repository: CRAN
Date/Publication: 2009-11-22 16:27:31

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New package log10 with initial version 0.0.3-05
Package: log10
Version: 0.0.3-05
Date: 2009-11-17
Title: Decimal log plotting
Author: Timothee Poisot
Maintainer: Timothee Poisot
Depends: R (>= 1.8.0)
Description: Provides a range of function for 10-log plotting
License: GPL (>= 2)
URL: http://homepage.mac.com/tim.poisot
Repository: CRAN
Repository/R-Forge/Project: scian
Repository/R-Forge/Revision: 19
Date/Publication: 2009-11-22 16:20:55
Packaged: 2009-11-19 21:20:33 UTC; rforge

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Package latentnet updated to version 2.2-3 with previous version 2.2-2 dated 2009-10-28

Author: Pavel N. Krivitsky , Mark S. Handcock , based on original code from "latentnetHRT", and code from other packages of `statnet' project
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster models for statistical networks.

Diff between latentnet versions 2.2-2 dated 2009-10-28 and 2.2-3 dated 2009-11-22

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Package igraph updated to version 0.5.3 with previous version 0.5.2-2 dated 2009-05-08

Author: Gabor Csardi
Title: Network analysis and visualization
Description: Routines for simple graphs and network analysis. igraph can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality indices and much more.

Diff between igraph versions 0.5.2-2 dated 2009-05-08 and 0.5.3 dated 2009-11-22

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Package ic.infer updated to version 1.1 with previous version 1.0-6 dated 2008-09-21

Author: Ulrike Groemping
Title: Inequality constrained inference in linear normal situations
Description: This package implements parameter estimation in normal (linear) models under linear equality and inequality constraints and implements normal likelihood ratio tests involving inequality-constrained hypotheses. For inequality-constrained linear models, averaging over R-squared for different orderings of regressors is also included.

Diff between ic.infer versions 1.0-6 dated 2008-09-21 and 1.1 dated 2009-11-22

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New package highlight with initial version 0.1-3
Package: highlight
Type: Package
Title: Syntax highlighter
Version: 0.1-3
Date: 2009-11-21
Author: Romain Francois
Maintainer: Romain Francois
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom sweave driver performing syntax highlighting of R code chunks
License: GPL (>= 3.0)
Depends: R (>= 2.10.0), codetools, utils, parser (>= 0.0-5)
LinkingTo: parser
Packaged: 2009-11-22 08:53:46 UTC; romain
Repository: CRAN
Date/Publication: 2009-11-22 16:20:30

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Package gap updated to version 1.0-21 with previous version 1.0-20 dated 2009-08-26

Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley
Title: Genetic analysis package
Description: It is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

Diff between gap versions 1.0-20 dated 2009-08-26 and 1.0-21 dated 2009-11-22

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New package gamlss.util with initial version 3.1-0
Package: gamlss.util
Description: Extra utilities for GAMLSS models.
Title: GAMLSS Utilities.
LazyLoad: yes
Version: 3.1-0
Date: 2009-11-22
Depends: R (>= 2.4.0), gamlss, colorspace, Matrix
Author: Mikis Stasinopoulos , Bob Rigby
Maintainer: Mikis Stasinopoulos
License: GPL-2 | GPL-3
URL: http://www.gamlss.com/
Packaged: 2009-11-22 13:26:21 UTC; stasinom
Repository: CRAN
Date/Publication: 2009-11-22 16:17:30

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Package gamlss.tr updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby
Title: Generating and fitting truncated (gamlss.family) distributions
Description: This is an add on package to GAMLSS. The purpose of this package is to allow users to defined truncated distributions in GAMLSS models. The main function gen.trun() generates truncated version of an existing GAMLSS family distribution.

Diff between gamlss.tr versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION   |    8 ++++----
 R/trun.d.R    |   30 +++++++++++++++---------------
 man/trun.d.Rd |   22 +++++++++++-----------
 3 files changed, 30 insertions(+), 30 deletions(-)

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Package gamlss.nl updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby with contributions from Philippe Lambert.
Title: Fitting non linear parametric GAMLSS models
Description: This is an add on package to GAMLSS. It allows one extra method for fitting GAMLSS models. The main function nlgamlss() can fit any parametric (up to four parameter) GAMLSS distribution.

Diff between gamlss.nl versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION |    8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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Package gamlss.mx updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby
Title: A GAMLSS add on package for fitting mixture distributions
Description: The main purpose of this package is to allow fitting of mixture distributions with GAMLSS models.

Diff between gamlss.mx versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION |    8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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Package gamlss.dist updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby with contributions from Calliope Akantziliotou, Gillian Heller, Raydonal Ospina and Nicoletta Motpan.
Title: Distributions to be used for GAMLSS modelling.
Description: This package contains the distributions for GAMLSS modelling.

Diff between gamlss.dist versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION |    8 ++++----
 man/GB1.Rd  |    6 +++---
 man/GB2.Rd  |    4 +++-
 3 files changed, 10 insertions(+), 8 deletions(-)

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Package gamlss.data updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby
Title: GAMLSS Data.
Description: Data for GAMLSS models.

Diff between gamlss.data versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION    |    8 ++++----
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Package gamlss.cens updated to version 3.1.0 with previous version 3.0.1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby , Nicoleta Mortan
Title: Fitting an interval response variable using gamlss.family distributions
Description: This is an add on package to GAMLSS. The purpose of this package is to allow users to fit interval response variables in GAMLSS models. The main function gen.cens() generates a censored version of an existing GAMLSS family distribution.

Diff between gamlss.cens versions 3.0.1 dated 2009-10-14 and 3.1.0 dated 2009-11-22

 DESCRIPTION |    8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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New package gamlss.add with initial version 3.1-0
Package: gamlss.add
Description: Extra additive terms for GAMLSS models.
Title: GAMLSS Additive.
LazyLoad: yes
Version: 3.1-0
Date: 2009-11-22
Depends: R (>= 2.4.0), gamlss, mgcv, nnet, gamlss.util
Author: Mikis Stasinopoulos , Bob Rigby
Maintainer: Mikis Stasinopoulos
License: GPL-2 | GPL-3
URL: http://www.gamlss.com/
Packaged: 2009-11-22 13:33:27 UTC; stasinom
Repository: CRAN
Date/Publication: 2009-11-22 16:17:07

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Package gamlss updated to version 3.1-0 with previous version 3.0-1 dated 2009-10-14

Author: Mikis Stasinopoulos , Bob Rigby with contributions from Calliope Akantziliotou.
Title: Generalized Additive Models for Location Scale and Shape.
Description: The library for fitting GAMLSS models.

Diff between gamlss versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22

 DESCRIPTION       |    8 ++++----
 NAMESPACE         |    3 ++-
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Package gRain updated to version 0.8.2 with previous version 0.8.1 dated 2009-08-01

Author: Søren Højsgaard
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).

Diff between gRain versions 0.8.1 dated 2009-08-01 and 0.8.2 dated 2009-11-22

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New package dvfBm with initial version 1.0
Package: dvfBm
Type: Package
Title: Discrete variations of a fractional Brownian motion
Version: 1.0
Date: 2009-10-14
Author: Jean-Francois Coeurjolly
Maintainer: J.-F. Coeurjolly
Description: Hurst exponent estimation of a fractional Brownian motion by using discrete variations methods in presence of outliers and/or an additive noise
License: GPL (>= 2.0)
LazyLoad: yes
Depends: wmtsa
Packaged: Fri Nov 20 14:34:09 2009; jeff
Repository: CRAN
Date/Publication: 2009-11-22 16:11:39

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Package diffusionMap updated to version 1.0-0 with previous version 0.0-2 dated 2009-05-10

Author: Joseph Richards
Title: Diffusion map
Description: Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model.

Diff between diffusionMap versions 0.0-2 dated 2009-05-10 and 1.0-0 dated 2009-11-22

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Package clinfun updated to version 0.8.7 with previous version 0.8.6 dated 2009-11-19

Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.

Diff between clinfun versions 0.8.6 dated 2009-11-19 and 0.8.7 dated 2009-11-22

 CHANGES     |    4 ++++
 DESCRIPTION |    6 +++---
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Package RcmdrPlugin.DoE updated to version 0.6-7 with previous version 0.6-6 dated 2009-10-26

Author: Ulrike Groemping
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.

Diff between RcmdrPlugin.DoE versions 0.6-6 dated 2009-10-26 and 0.6-7 dated 2009-11-22

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Package Matrix updated to version 0.999375-32 with previous version 0.999375-31 dated 2009-10-08

Author: Douglas Bates and Martin Maechler
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and operations on them using Lapack and SuiteSparse.

Diff between Matrix versions 0.999375-31 dated 2009-10-08 and 0.999375-32 dated 2009-11-22

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Package HistData updated to version 0.6-5 with previous version 0.6-4 dated 2009-11-13

Author: Michael Friendly, with contributions by Stephane Dray, Hadley Wickham
Title: Data sets from the history of statistics and data visualization
Description: The HistData package provides a collection of small data sets that are interesting and important in the history of statistics and data visualization. The goal of the package is to make these available, both for instructional use and for historical research. Some of these present interesting challenges for graphics or analysis in R.

Diff between HistData versions 0.6-4 dated 2009-11-13 and 0.6-5 dated 2009-11-22

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Package Epi updated to version 1.1.9 with previous version 1.1.7 dated 2009-09-30

Author: Bendix Carstensen, Martyn Plummer, Esa Laara, Michael Hills et. al.
Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, including interval censored data and representation of multistate data. Also some useful functions for tabulation and plotting. Contains some epidemiological datasets.

Diff between Epi versions 1.1.7 dated 2009-09-30 and 1.1.9 dated 2009-11-22

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 DESCRIPTION            |   10 -
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Fri, 20 Nov 2009

Package waveclock updated to version 1.0-4 with previous version 1.0-3.1 dated 2009-02-23

Author: Tom Price
Title: Time-frequency analysis of cycling cell luminescence data
Description: waveclock is an R function designed to assess the period and amplitude of cycling cell luminescence data. The function reconstructs the modal frequencies from a continuous wavelet decomposition of the luminescence data using the 'crazy climbers' algorithm described in "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

Diff between waveclock versions 1.0-3.1 dated 2009-02-23 and 1.0-4 dated 2009-11-20

 CHANGES               |   42 +++--
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Package titan updated to version 1.0-16 with previous version 1.0-15.1 dated 2009-02-23

Author: Tom Price
Title: Titration analysis for mass spectrometry data
Description: GUI to analyze mass spectrometric data on the relative abundance of two substances from a titration series.

Diff between titan versions 1.0-15.1 dated 2009-02-23 and 1.0-16 dated 2009-11-20

 Changes        |   19 +-
 DESCRIPTION    |   28 ++-
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Package sp updated to version 0.9-47 with previous version 0.9-44 dated 2009-09-18

Author: Edzer J. Pebesma , Roger Bivand and others
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.

Diff between sp versions 0.9-44 dated 2009-09-18 and 0.9-47 dated 2009-11-20

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Package quadprog updated to version 1.4-12 with previous version 1.4-11 dated 2007-07-13

Author: S original by Berwin A. Turlach R port by Andreas Weingessel
Title: Functions to solve Quadratic Programming Problems.
Description: This package contains routines and documentation for solving quadratic programming problems.

Diff between quadprog versions 1.4-11 dated 2007-07-13 and 1.4-12 dated 2009-11-20

 ChangeLog               |    8 ++
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 R/quadprog.R            |    2 
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Package cgh updated to version 1.0-7 with previous version 1.0-6.1 dated 2009-02-23

Author: Tom Price
Title: Microarray CGH analysis using the Smith-Waterman algorithm
Description: Functions to analyze microarray comparative genome hybridization data using the Smith-Waterman algorithm

Diff between cgh versions 1.0-6.1 dated 2009-02-23 and 1.0-7 dated 2009-11-20

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Package rtv updated to version 0.3.1 with previous version 0.3.0 dated 2009-08-20

Author: CHARLOTTE MAIA
Title: Random Time Variables
Description: An R package for conveniently representing, manipulating and visualising realisations of random time variables. This package is pending a major rewrite.

Diff between rtv versions 0.3.0 dated 2009-08-20 and 0.3.1 dated 2009-11-20

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Package rrv updated to version 0.0.2 with previous version 0.0.1 dated 2009-08-20

Author: CHARLOTTE MAIA
Title: Random Return Variables
Description: An incomplete R package for working with random return variables. The current package provides limited support for formatting money. More features are planned for the future.

Diff between rrv versions 0.0.1 dated 2009-08-20 and 0.0.2 dated 2009-11-20

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Package rpubchem updated to version 1.4.3 with previous version 1.4.2 dated 2009-02-08

Author: Rajarshi Guha
Title: rpubchem - Interface to the PubChem Collection
Description: Access PubChem data (compounds, substance, assays). Structural information is provided in the form of SMILES strings. This package only provides access to a subset of the precalculated data stored by PubChem. Bio-assay data can be accessed to obtain descriptions as well as the actual data. It is also possible to search for assay ID's by keyword. Currently the main limitation is that only 1000 molecules can be downloaded at a time from the PubChem servers

Diff between rpubchem versions 1.4.2 dated 2009-02-08 and 1.4.3 dated 2009-11-20

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Package meboot updated to version 1.0-2 with previous version 1.0-1 dated 2009-09-29

Author: Hrishikesh D. Vinod and Javier López-de-Lacalle
Title: Maximum Entropy Bootstrap for Time Series
Description: This package performs maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. The reference paper (Vinod, H.D., 2004) explains how the algorithm satisfies the ergodic theorem and the central limit theorem.

Diff between meboot versions 1.0-1 dated 2009-09-29 and 1.0-2 dated 2009-11-20

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Package fdrtool updated to version 1.2.6 with previous version 1.2.5 dated 2008-07-07

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

Diff between fdrtool versions 1.2.5 dated 2008-07-07 and 1.2.6 dated 2009-11-20

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Package dclone updated to version 1.0-0 with previous version 0.9-0 dated 2009-11-05

Author: Peter Solymos
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.

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New package amba with initial version 0.2.0
Package: amba
Title: Additive Models for Business Applications
Version: 0.2.0
Date: 2009-11-19
Author: CHARLOTTE MAIA
Maintainer: Charlotte Maia
Description: Additive models with a strong technical focus on term objects, model selection (semiparametric), missing explanatory values and interpretation. These models are restricted to vaguely-normal responses, plus have very little support for correlated explanatories and statistical inference. This package is not complete.
License: GPL (>= 2)
Depends: oosp (>= 0.2.0)
Packaged: 2009-11-19 06:56:04 UTC; maia
Repository: CRAN
Date/Publication: 2009-11-20 07:53:15

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Thu, 19 Nov 2009

Package mixer updated to version 1.0 with previous version 0.2 dated 2008-10-15

Author: Christophe Ambroise, Gilles Grasseau, Mark Hoebeke, Pierre Latouche, Vincent Miele, Franck Picard
Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of networks using MIXtures of Erdos-Renyi random graphs

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Package clinfun updated to version 0.8.6 with previous version 0.8.5 dated 2009-07-18

Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.

Diff between clinfun versions 0.8.5 dated 2009-07-18 and 0.8.6 dated 2009-11-19

 CHANGES        |    6 ++++++
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Package marelacTeaching updated to version 1.1 with previous version 1.0 dated 2009-09-07

Author: Karline Soetaert , Filip Meysman
Title: Datasets and tutorials for use in aquatic sciences
Description: Datasets and tutorials for use in the MArine, Riverine, Estuarine, LAcustrine and Coastal sciences

Diff between marelacTeaching versions 1.0 dated 2009-09-07 and 1.1 dated 2009-11-19

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Package intamap updated to version 1.3-1 with previous version 1.2-18 dated 2009-09-28

Author: Edzer Pebesma , Jon Skoien and others
Title: procedures for automated interpolation
Description: A package that provides classes and methods for automated spatial interpolation.

Diff between intamap versions 1.2-18 dated 2009-09-28 and 1.3-1 dated 2009-11-19

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New package TGUICore with initial version 0.9.2
Package: TGUICore
Type: Package
Title: Teaching GUI - Core functionality
Version: 0.9.2
Date: 2009-11-19
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Maintainer: Alexander Kowarik
Description: Trainings-GUI
Depends: tcltk, tkrplot, utils
License: GPL
Packaged: 2009-11-19 13:11:09 UTC; alex
Repository: CRAN
Date/Publication: 2009-11-19 16:33:36

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New package TGUITeaching with initial version 0.9.2
Package: TGUITeaching
Type: Package
Title: Teaching GUI - prototype
Version: 0.9.2
Date: 2009-11-19
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Maintainer: Bernhard Meindl
Description: Trainings-GUI
License: GPL
Depends: TGUICore, tcltk, tkrplot
Packaged: 2009-11-19 13:16:50 UTC; alex
Repository: CRAN
Date/Publication: 2009-11-19 16:33:37

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Package zoo updated to version 1.6-1 with previous version 1.6-0 dated 2009-11-17

Author: Achim Zeileis, Gabor Grothendieck
Title: 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.

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Package WMCapacity updated to version 0.9.1 with previous version 0.9 dated 2009-10-05

Author: Richard D. Morey
Title: GUI implementing Bayesian working memory models
Description: A GUI R implementation of hierarchical Bayesian models of working memory, used for analyzing change detection data.

Diff between WMCapacity versions 0.9 dated 2009-10-05 and 0.9.1 dated 2009-11-19

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Package VPdtw updated to version 2.1-4 with previous version 2.1-3 dated 2009-11-18

Author: David Clifford, Glenn Stone
Title: Variable Penalty Dynamic Time Warping
Description: Variable Penalty Dynamic Time Warping for aligning GC-MS chromatograms to a master signal and more. With the appropriate penalty this method performs good alignment without altering the shape of peaks in GC-MS data.

Diff between VPdtw versions 2.1-3 dated 2009-11-18 and 2.1-4 dated 2009-11-19

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Package VLMC updated to version 1.3-11 with previous version 1.3-10 dated 2006-09-18

Author: Martin Maechler
Title: VLMC -- Variable Length Markov Chains
Description: Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of VLMC -- Variable Length Markov Chain -- Models

Diff between VLMC versions 1.3-10 dated 2006-09-18 and 1.3-11 dated 2009-11-19

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Package tuneR updated to version 0.2-12 with previous version 0.2-11 dated 2009-10-15

Author: Uwe Ligges with contributions from Andrea Preusser and Claus Weihs, as well as code fragments and ideas from the former package 'sound' by Matthias Heymann.
Title: Analysis of music
Description: Collection of tools to analyze music, handling wave files, transcription, ...

Diff between tuneR versions 0.2-11 dated 2009-10-15 and 0.2-12 dated 2009-11-19

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Package tis updated to version 1.8 with previous version 1.7 dated 2009-07-28

Author: Jeff Hallman
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.

Diff between tis versions 1.7 dated 2009-07-28 and 1.8 dated 2009-11-19

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Package sspir updated to version 0.2.8 with previous version 0.2.7 dated 2009-08-10

Author: Claus Dethlefsen, Soren Lundbye-Christensen and Anette Luther Christensen
Title: State Space Models in R
Description: A glm-like formula language to define dynamic generalized linear models (state space models). Includes functions for Kalman filtering and smoothing. Estimation of variance matrices can be perfomred using the EM algorithm in case of Gaussian models. Read help(sspir) to get started.

Diff between sspir versions 0.2.7 dated 2009-08-10 and 0.2.8 dated 2009-11-19

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Package REQS updated to version 0.8-5 with previous version 0.8-4 dated 2009-08-30

Author: Patrick Mair, Eric Wu
Title: R/EQS Interface
Description: This package contains the function run.eqs() which calls an EQS script file, executes the EQS estimation, and, finally, imports the results as R objects. These two steps can be performed separately: call.eqs() calls and executes EQS, whereas read.eqs() imports existing EQS outputs as objects into R.

Diff between REQS versions 0.8-4 dated 2009-08-30 and 0.8-5 dated 2009-11-19

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Package pscl updated to version 1.03.2 with previous version 1.03 dated 2009-01-27

Author: Simon Jackman, with contributions from Alex Tahk, Achim Zeileis, Christina Maimone and Jim Fearon
Title: Political Science Computational Laboratory, Stanford University
Description: Bayesian analysis of item-response theory (IRT) models, roll call analysis; computing highest density regions; maximum likelihood estimation of zero-inflated and hurdle models for count data; goodness-of-fit measures for GLMs; data sets used in writing and teaching at the Political Science Computational Laboratory; seats-votes curves.

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Package MiscPsycho updated to version 1.5 with previous version 1.4 dated 2009-03-10

Author: Harold C. Doran
Title: Miscellaneous Psychometric Analyses
Description: Miscellaneous functions for psychometric problems

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Package longmemo updated to version 0.9-7 with previous version 0.9-6 dated 2009-01-11

Author: S scripts originally by Jan Beran Datasets via Brandon Whitcher . Toplevel R functions and much more by Martin Maechler.
Title: Statistics for Long-Memory Processes (Jan Beran) -- Data and Functions
Description: Datasets and Functionality from the textbook Jan Beran (1994). Statistics for Long-Memory Processes; Chapman \& Hall.

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Package fame updated to version 2.7 with previous version 2.6 dated 2009-04-14

Author: Jeff Hallman
Title: Interface for FAME time series database
Description: Read and write FAME databases.

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Package ctv updated to version 0.5-6 with previous version 0.5-4 dated 2009-09-30

Author: Achim Zeileis, Kurt Hornik
Title: CRAN Task Views
Description: Server-side and client-side tools for task views to CRAN-style repositories

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Package candisc updated to version 0.5-16 with previous version 0.5-15 dated 2009-06-14

Author: Michael Friendly and John Fox
Title: Generalized Canonical Discriminant Analysis
Description: Functions for computing and graphing canonical discriminant analyses.

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Wed, 18 Nov 2009

Package mgcv updated to version 1.6-0 with previous version 1.5-6 dated 2009-09-12

Author: Simon Wood
Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.

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Package gamm4 updated to version 0.0-2 with previous version 0.0-1 dated 2009-09-07

Author: Simon Wood
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.

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Package sfsmisc updated to version 1.0-9 with previous version 1.0-8 dated 2009-08-10

Author: Martin Maechler and many others.
Title: Utilities from Seminar fuer Statistik ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, many ported from S-plus times.

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Package robustbase updated to version 0.5-0 with previous version 0.4-5 dated 2009-01-18

Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov , Andreas Ruckstuhl , Matias Salibian-Barrera , Tobias Verbeke , Martin Maechler
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. The goal is to provide tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.

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Package robustX updated to version 1.1-1 with previous version 1.1-0 dated 2009-06-14

Author: Werner Stahel, Martin Maechler and potentially others
Title: eXperimental eXtraneous eXtraordinary ... Functionality for Robust Statistics
Description: eXperimental eXtraneous eXtraordinary Functionality for Robust Statistics

Diff between robustX versions 1.1-0 dated 2009-06-14 and 1.1-1 dated 2009-11-18

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Package polySegratioMM updated to version 0.5-2 with previous version 0.5-1 dated 2009-11-17

Author: Peter Baker
Title: Bayesian mixture models for marker dosage in autopolyploids
Description: Fits Bayesian mixture models to estimate marker dosage for dominant markers on autopolyploids using JAGS (1.0 or greater). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods

Diff between polySegratioMM versions 0.5-1 dated 2009-11-17 and 0.5-2 dated 2009-11-18

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Package polySegratio updated to version 0.2-2 with previous version 0.2-1 dated 2009-11-17

Author: Peter Baker
Title: Simulate and test marker dosage for dominant markers in autopolyploids
Description: Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.

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New package miniGUI with initial version 0.2.0
Package: miniGUI
Title: tktcl quick and simple function GUI.
Version: 0.2.0
Date: 2007-10-01
Depends: R (>= 2.5.0), tcltk
Author: Jorge Luis Ojeda Cabrera
Description: quick and simple tktcl miniGUI to call functions.
Maintainer: Jorge Luis Ojeda Cabrera
License: GPL
Packaged: 2009-11-18 12:38:04 UTC; jorge
Repository: CRAN
Date/Publication: 2009-11-18 14:00:55

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Package mboost updated to version 1.1-4 with previous version 1.1-3 dated 2009-09-23

Author: Torsten Hothorn, Peter Buhlmann, Thomas Kneib, Matthias Schmid and Benjamin Hofner
Title: Model-Based Boosting
Description: Functional gradient descent algorithms (boosting) for optimizing general loss functions utilizing componentwise least squares, either of parametric linear form or smoothing splines, or regression trees as base learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.

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Package classGraph updated to version 0.7-3 with previous version 0.7-2 dated 2009-04-15

Author: Martin Maechler partly based on code from Robert Gentleman
Title: Construct Graphs of S4 Class Hierarchies
Description: Construct directed graphs of S4 class hierarchies and visualize them. In general, these graphs typically are DAGs (directed acyclic graphs), often simple trees in practice.

Diff between classGraph versions 0.7-2 dated 2009-04-15 and 0.7-3 dated 2009-11-18

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Package AquaEnv updated to version 0.8 with previous version 0.7 dated 2009-03-31

Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Title: AquaEnv - an integrated development toolbox for aquatic chemical model generation
Description: AquaEnv is an integrated development toolbox for aquatic chemical model generation focused on (ocean) acidification and CO2 air-water exchange. It contains all elements necessary to model the pH, the related CO2 air-water exchange, as well as aquatic acid-base chemistry in general for an arbitrary marine, estuarine or freshwater system. Also chemical batches can be modelled. Next to the routines necessary to calculate desired information, AquaEnv also contains a suite of tools to visualize this information. Furthermore, AquaEnv can not only be used to build dynamic models of aquatic systems, but it can also serve as a simple desktop tool for the experimental aquatic chemist to generate and visualize all possible derived information from a set of measurements with one single easy to use R function. Additionally, the sensitivity of the system to variations in the input variables can be visualized.

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Package lordif updated to version 0.1-4 with previous version 0.1-3 dated 2009-11-05

Author: Seung W. Choi, with contributions from Laura E. Gibbons and Paul K. Crane
Title: Logistic Regression Differential Item Functioning using IRT
Description: Analysis of Differential Item Functioning (DIF) for dichotomous and polytomous items using an iterative hybrid of (ordinal) logistic regression and item response theory (IRT).

Diff between lordif versions 0.1-3 dated 2009-11-05 and 0.1-4 dated 2009-11-18

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More information about lordif at CRAN
Permanent link

New package VPdtw with initial version 2.1-3
Package: VPdtw
Type: Package
Title: Variable Penalty Dynamic Time Warping
Version: 2.1-3
Date: 2009-11-18
Author: David Clifford, Glenn Stone
Maintainer: David Clifford
Description: Variable Penalty Dynamic Time Warping for aligning GC-MS chromatograms to a master signal and more. With the appropriate penalty this method performs good alignment without altering the shape of peaks in GC-MS data.
License: GPL-2
Packaged: Wed Nov 18 18:04:10 2009; cli065
Repository: CRAN
Date/Publication: 2009-11-18 07:57:20

More information about VPdtw at CRAN
Permanent link

Package FrF2 updated to version 1.0-1 with previous version 1.0 dated 2009-10-08

Author: Ulrike Groemping
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.

Diff between FrF2 versions 1.0 dated 2009-10-08 and 1.0-1 dated 2009-11-18

 DESCRIPTION               |    8 ++++----
 R/DanielPlot.R            |   14 ++++++++++++--
 inst/NEWS                 |    8 ++++++++
 man/CatalogueAccessors.Rd |   16 ++++++++--------
 4 files changed, 32 insertions(+), 14 deletions(-)

More information about FrF2 at CRAN
Permanent link

Tue, 17 Nov 2009

Package zoo updated to version 1.6-0 with previous version 1.5-8 dated 2009-07-22

Author: Achim Zeileis, Gabor Grothendieck
Title: 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.

Diff between zoo versions 1.5-8 dated 2009-07-22 and 1.6-0 dated 2009-11-17

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More information about zoo at CRAN
Permanent link

Package sandwich updated to version 2.2-2 with previous version 2.2-1 dated 2009-02-05

Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series and longitudinal data.

Diff between sandwich versions 2.2-1 dated 2009-02-05 and 2.2-2 dated 2009-11-17

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More information about sandwich at CRAN
Permanent link

Package lmtest updated to version 0.9-25 with previous version 0.9-24 dated 2009-05-28

Author: Torsten Hothorn, Achim Zeileis, Giovanni Millo, David Mitchell
Title: Testing Linear Regression Models
Description: A collection of tests, data sets and examples for diagnostic checking in linear regression models.

Diff between lmtest versions 0.9-24 dated 2009-05-28 and 0.9-25 dated 2009-11-17

 DESCRIPTION                 |    8 ++++----
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More information about lmtest at CRAN
Permanent link

Package fxregime updated to version 0.3-1 with previous version 0.3-0 dated 2009-08-28

Author: Achim Zeileis, Ajay Shah, Ila Patnaik
Title: Exchange Rate Regime Analysis
Description: Exchange rate regression and structural change tools for estimating, testing, dating, and monitoring (de facto) exchange rate regimes.

Diff between fxregime versions 0.3-0 dated 2009-08-28 and 0.3-1 dated 2009-11-17

 DESCRIPTION              |    8 ++++----
 NEWS                     |    5 +++++
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More information about fxregime at CRAN
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New package testthat with initial version 0.1
Package: testthat
Type: Package
Title: Tools for splitting, applying and combining data
Version: 0.1
Author: Hadley Wickham
Maintainer: Hadley Wickham
Description: Test_that code. Tools to make testing fun :)
URL: http://had.co.nz/
Depends: R (>= 2.8), mutatr, digest
License: GPL
LazyData: true
Collate: 'aaa-classes.r' 'auto-test.r' 'colour-text.r' 'context.r' 'expect-that.r' 'expectation.r' 'expectations.r' 'library.r' 'reporter-minimal.r' 'reporter-stop.r' 'reporter-summary.r' 'reporter-zzz.r' 'reporter.r' 'test-files.r' 'test-that.r' 'watcher.r'
Packaged: 2009-11-17 19:18:05 UTC; hornik
Repository: CRAN
Date/Publication: 2009-11-17 19:18:56

More information about testthat at CRAN
Permanent link

Package Runuran updated to version 0.11.0 with previous version 0.10.1 dated 2009-08-06

Author: Josef Leydold and Wolfgang H\"ormann
Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators

Diff between Runuran versions 0.10.1 dated 2009-08-06 and 0.11.0 dated 2009-11-17

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More information about Runuran at CRAN
Permanent link

Package rstream updated to version 1.2.4 with previous version 1.2.3 dated 2009-01-08

Author: Josef Leydold
Title: Streams of random numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.

Diff between rstream versions 1.2.3 dated 2009-01-08 and 1.2.4 dated 2009-11-17

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More information about rstream at CRAN
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Package monomvn updated to version 1.7-4 with previous version 1.7-3 dated 2009-08-19

Author: Robert B. Gramacy
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) prior 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) and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided

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Package clues updated to version 0.3.9 with previous version 0.3.2 dated 2009-03-17

Author: Fang Chang , Vincent Carey , Weiliang Qiu , Ruben H. Zamar , Ross Lazarus , Xiaogang Wang
Title: Clustering Method Based on Local Shrinking
Description: The package contains functions for automatically estimating the number of clusters and getting the final cluster partition without any input parameter except the stopping rule for convergence. The package also provides functions to evaluate and compare the performances of partitions of a data set both numerically and graphically.

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New package polySegratioMM with initial version 0.5-1
Package: polySegratioMM
Type: Package
Title: Bayesian mixture models for marker dosage in autopolyploids
Version: 0.5-1
Date: 2008-07-18
Author: Peter Baker
Maintainer: Peter Baker
Depends: polySegratio, coda
Imports: gtools
Description: Fits Bayesian mixture models to estimate marker dosage for dominant markers on autopolyploids using JAGS (1.0 or greater). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods
License: GPL-2
Packaged: 2009-11-17 16:05:43 UTC; pete
Repository: CRAN
Date/Publication: 2009-11-17 17:24:35

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Package nnDiag updated to version 0.0-3 with previous version 0.0-2 dated 2009-11-16

Author: Brian Walters , Zhen Zhang , Andrew O. Finley
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN classifications.

Diff between nnDiag versions 0.0-2 dated 2009-11-16 and 0.0-3 dated 2009-11-17

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New package polySegratio with initial version 0.2-1
Package: polySegratio
Type: Package
Title: Simulate and test marker dosage for dominant markers in autopolyploids
Version: 0.2-1
Date: 2008-01-09
Depends: gdata
Author: Peter Baker
Maintainer: Peter Baker
Description: Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.
License: GPL-2
Packaged: 2009-11-17 16:23:49 UTC; pete
Repository: CRAN
Date/Publication: 2009-11-17 17:24:31

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Package iGenomicViewer updated to version 2.4.6 with previous version 2.4.4 dated 2009-10-29

Author: Daniel P Gaile , Lori A. Shepherd , Lara Sucheston , Andrew Bruno , Kenneth F. Manly
Title: Tool for sending interactive bioinformatic heatmaps with tool-tip content.
Description: A tool for visualizing data

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Package untb updated to version 1.6-2 with previous version 1.6-1 dated 2009-10-15

Author: Robin K. S. Hankin
Title: ecological drift under the UNTB
Description: A collection of utilities for biodiversity data. Includes the simulation of ecological drift under Hubbell's Unified Neutral Theory of Biodiversity, and the calculation of various diagnostics such as Preston curves. Now includes functionality provided by Francois Munoz and Andrea Manica.

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Package parcor updated to version 0.2-1 with previous version 0.2 dated 2009-11-12

Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression.

Diff between parcor versions 0.2 dated 2009-11-12 and 0.2-1 dated 2009-11-17

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Package automap updated to version 1.0-4 with previous version 1.0-2 dated 2009-07-18

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

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Package tweedie updated to version 2.0.2 with previous version 2.0.0 dated 2009-08-10

Author: Peter K Dunn
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.

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Package seqinr updated to version 2.0-7 with previous version 2.0-6 dated 2009-10-18

Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data management under the ACNUC system.

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Package sca updated to version 0.8-7 with previous version 0.8-6 dated 2009-02-09

Author: Valentin Rousson and Martin Maechler
Title: Simple Component Analysis
Description: Simple Component Analysis often provides much more interpretable components than Principal Components (PCA) without losing too much.

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Package RcmdrPlugin.Export updated to version 0.3-0 with previous version 0.2-2 dated 2009-10-14

Author: Liviu Andronic
Title: Graphically export output to LaTeX or HTML
Description: The package helps users to graphically export Rcmdr output to LaTeX or HTML code, via xtable() or Hmisc::latex(). The plug-in was originally intended to facilitate exporting Rcmdr output to formats other than ASCII text and to provide R novices with an easy-to-use, easy-to-access reference on exporting R objects to formats suited for printed output. The package documentation contains several pointers on creating reports, either by using conventional word processors or LaTeX/LyX.

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Package DRI updated to version 1.1 with previous version 1.0 dated 2009-08-05

Author: Keyan Salari, Robert Tibshirani, Jonathan R. Pollack
Title: DR-Integrator
Description: Integrative analysis of DNA copy number and gene expression data described in Salari et al 2009

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Package Amelia updated to version 1.2-14 with previous version 1.2-13 dated 2009-08-13

Author: James Honaker , Gary King , Matthew Blackwell
Title: Amelia II: A Program for Missing Data
Description: Amelia II "multiply imputes" missing data in a single cross-section (such as a survey), from a time series (like variables collected for each year in a country), or from a time-series-cross-sectional data set (such as collected by years for each of several countries). Amelia II implements our bootstrapping-based algorithm that gives essentially the same answers as the standard IP or EMis approaches, is usually considerably faster than existing approaches and can handle many more variables. Unlike Amelia I and other statistically rigorous imputation software, it virtually never crashes (but please let us know if you find to the contrary!). The program also generalizes existing approaches by allowing for trends in time series across observations within a cross-sectional unit, as well as priors that allow experts to incorporate beliefs they have about the values of missing cells in their data. Amelia II also includes useful diagnostics of the fit of multiple imputation models. The program works from the R command line or via a graphical user interface that does not require users to know R.

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Mon, 16 Nov 2009

Package stringr updated to version 0.2 with previous version 0.1.10 dated 2009-11-09

Author: Hadley Wickham
Title: Make it easier to work with strings.
Description: stringr is a set of simple wrappers that make R's string functions more consistent, simpler and easier to use. It does this by ensuring that: function and argument names (and positions) are consistent, all functions deal with NA's and zero length character appropriately, and the output data structures from each function matches the input data structures of other functions.

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Package nnDiag updated to version 0.0-2 with previous version 0.0-1 dated 2009-10-26

Author: Brian Walters , Zhen Zhang , Andrew O. Finley
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN classifications.

Diff between nnDiag versions 0.0-1 dated 2009-10-26 and 0.0-2 dated 2009-11-16

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Package klaR updated to version 0.6-1 with previous version 0.6-0 dated 2009-09-22

Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero Szepannek, Marc Zentgraf
Title: Classification and visualization
Description: Miscellaneous functions for classification and visualization developed at the Fakultaet Statistik, Technische Universitaet Dortmund

Diff between klaR versions 0.6-0 dated 2009-09-22 and 0.6-1 dated 2009-11-16

 Changes-ToDo  |    8 +++-----
 DESCRIPTION   |    8 ++++----
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Package fpc updated to version 1.2-7 with previous version 1.2-6 dated 2009-08-26

Author: Christian Hennig
Title: Fixed point clusters, clusterwise regression and discriminant plots
Description: Fuzzy and crisp fixed point cluster analysis based on Mahalanobis distance and linear regression fixed point clusters. Semi-explorative, semi-model-based clustering methods, operating on n*p data, do not need prespecification of number of clusters, produce overlapping clusters. Symmetric and asymmetric discriminant projections separate groups optimally, used to visualize the separation of groupings, visual cluster validation. Clusterwise linear regression by normal mixture modeling. Cluster validation statistics for distance based clustering including corrected Rand index. Clusterwise cluster stability assessment. DBSCAN clustering. Interface functions for many clustering methods implemented in R. Note that the use of the package mclust (called by function prabclust) is protected by a special license, see http://www.stat.washington.edu/mclust/license.txt, particularly point 6.

Diff between fpc versions 1.2-6 dated 2009-08-26 and 1.2-7 dated 2009-11-16

 DESCRIPTION              |   12 -
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Package RPMM updated to version 1.05 with previous version 1.0 dated 2009-09-09

Author: E. Andres Houseman, Sc.D.
Title: Recursively Partitioned Mixture Model
Description: Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.

Diff between RPMM versions 1.0 dated 2009-09-09 and 1.05 dated 2009-11-16

 DESCRIPTION   |    8 -
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 3 files changed, 154 insertions(+), 145 deletions(-)

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New package plsdof with initial version 0.1
Package: plsdof
Type: Package
Title: Degrees of Freedom for Partial Least Squares Regression
Version: 0.1
Date: 2009-11-16
Author: Nicole Kraemer, Mikio L. Braun
Maintainer: Nicole Kraemer
Description: The \code{psldof} package provides Degrees of Freedom estimates for Kernel Partial Least Squares Regression and its kernel extension. The package also provides model selection based on various information criteria (aic, bic, gmdl) and based on cross-validation.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-16 10:58:31 UTC; kranic
Repository: CRAN
Date/Publication: 2009-11-16 13:19:30

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Package r4ss updated to version 1.01 with previous version 1.0 dated 2009-11-10

Author: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, John Wallace, and other contributors
Title: R code for Stock Synthesis
Description: Functions for reading output, plotting, exploring and manipulating input files for Richard Methot's Stock Synthesis fisheries stock assessment modeling platform.

Diff between r4ss versions 1.0 dated 2009-11-10 and 1.01 dated 2009-11-16

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New package ibr with initial version 1.2
Package: ibr
Version: 1.2
Date: 2008-11-12
Title: Iterative Bias Reduction
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: Pierre-Andre Cornillon
Depends: fields
Description: an R package for multivariate smoothing
License: GPL (>= 2)
Packaged: 2009-11-16 09:36:51 UTC; pac
Repository: CRAN
Date/Publication: 2009-11-16 11:09:54

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New package mutatr with initial version 0.1
Package: mutatr
Type: Package
Title: Mutable objects for R.
Version: 0.1
Author: Hadley Wickham
Maintainer: Hadley Wickham
Description: Mutable prototype based objects with multiple inheritance.
URL: http://had.co.nz/
Depends: digest
License: GPL
LazyData: true
Collate: 'ancestors.r' 'core.r' 'object.r' 'object-inheritance.r' 'utils.r'
Packaged: 2009-11-16 05:09:53 UTC; hadley
Repository: CRAN
Date/Publication: 2009-11-16 07:44:57

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Package deldir updated to version 0.0-10 with previous version 0.0-9 dated 2009-11-04

Author: Rolf Turner
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set.

Diff between deldir versions 0.0-9 dated 2009-11-04 and 0.0-10 dated 2009-11-16

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New package BoolNet with initial version 1.3
Package: BoolNet
Type: Package
Title: Generation, reconstruction, simulation and analysis of Boolean networks
Version: 1.3
Date: 2009-10-02
Author: Christoph Muessel, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler
Suggests: igraph
Description: Provides methods to reconstruct and generate Boolean networks, and to analyze and visualize attractors in Boolean networks
License: Artistic-2.0
LazyLoad: yes
Packaged: 2009-11-15 20:04:20 UTC; muessel
Repository: CRAN
Date/Publication: 2009-11-16 07:44:50

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Sun, 15 Nov 2009

Package spgrass6 updated to version 0.6-12 with previous version 0.6-11 dated 2009-10-30

Author: Roger Bivand
Title: Interface between GRASS 6 geographical information system and R
Description: Interpreted interface between GRASS 6 geographical information system and R, based on starting R from within the GRASS environment, or running free-standing R in a temporary GRASS location; the package provides facilities for using all GRASS commands from the R command line.

Diff between spgrass6 versions 0.6-11 dated 2009-10-30 and 0.6-12 dated 2009-11-15

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 DESCRIPTION      |    8 +--
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New package profdpm with initial version 1.0
Package: profdpm
Type: Package
Title: Profile Dirichlet Process Mixtures
Version: 1.0
Date: 2009-04-09
Author: Matt Shotwell
Maintainer: Matt Shotwell
Description: This package performs profile inference for models utilizing the Dirichlet process (DP) and Dirichlet motivated process (DMP) mixtures. This method is not based on Markov chain Monte Carlo methods, as are most other mechanisms of inference in DP and DMP mixtures. This method searches for the maximum posterior (MAP) estimate for the cluster indicators in the DP or DMP mixture model.
License: GPL
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: profdpm
Repository/R-Forge/Revision: 51
Date/Publication: 2009-11-15 13:51:28
Packaged: 2009-11-11 21:13:17 UTC; rforge

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Package pomp updated to version 0.25-7 with previous version 0.25-4 dated 2009-09-22

Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes

Diff between pomp versions 0.25-4 dated 2009-09-22 and 0.25-7 dated 2009-11-15

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Package mefa updated to version 3.1-4 with previous version 3.1-3 dated 2009-10-15

Author: Peter Solymos
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.

Diff between mefa versions 3.1-3 dated 2009-10-15 and 3.1-4 dated 2009-11-15

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Package flashClust updated to version 0.10-1 with previous version 0.10 dated 2009-02-05

Author: code by Fionn Murtagh and R development team, modifications and packaging by Peter Langfelder
Title: Implementation of optimal hierarchical clustering
Description: Implementation of optimal hierarchical clustering

Diff between flashClust versions 0.10 dated 2009-02-05 and 0.10-1 dated 2009-11-15

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Package estout updated to version 0.8-1 with previous version 0.7-1 dated 2009-11-11

Author: Felix Kaminsky , inspired by the estout package for Stata.
Title: Estimates Output
Description: The function collection stores the estimates of several models and formats it to a table of the form estimate starred and std.err. below. The default output is LaTeX but output to CSV for later editing in a spreadsheet tool is possible as well. It works for linear models (lm) and panel models from the "plm"-package (plm). The added "descsto" and "desctab" enable you to export descriptive statistics of data-frames and single variables to LaTeX and CSV.

Diff between estout versions 0.7-1 dated 2009-11-11 and 0.8-1 dated 2009-11-15

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Package cshapes updated to version 0.1-2 with previous version 0.1-1 dated 2009-08-13

Author: Nils B. Weidmann , Doreen Kuse , Kristian Skrede Gleditsch
Title: CShapes Dataset and Utilities
Description: Package for CShapes, a GIS dataset of country boundaries (1946-2008). Includes functions for data extraction and the computation of weights matrices.

Diff between cshapes versions 0.1-1 dated 2009-08-13 and 0.1-2 dated 2009-11-15

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Package cmprskContin updated to version 1.5 with previous version 1.3 dated 2009-08-28

Author: Peter Gilbert, Ian McKeague, and Yanqing Sun
Title: Continuous mark-specific relative risks for two groups
Description: Estimation and testing of continuous mark-specific relative risks in two groups as described in Gilbert, P., McKeague, I. and Sun, Y. (2008) The 2-sample problem for failure rates depending on a continuous mark: an application to vaccine efficacy. Biostatistics 9, 2, 263-276. This package implements the methods presented in the paper for testing mark-specific hazards ratios and for estimation of mark-specific incidence ratios that are cumulative in time or cumulative in both time and the continuous mark.

Diff between cmprskContin versions 1.3 dated 2009-08-28 and 1.5 dated 2009-11-15

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Fri, 13 Nov 2009

Package survcomp updated to version 1.1.3 with previous version 1.1.2 dated 2009-06-05

Author: Benjamin Haibe-Kains, Christos Sotiriou, Gianluca Bontempi
Title: Performance Assessment and Comparison for Survival Analysis
Description: R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Diff between survcomp versions 1.1.2 dated 2009-06-05 and 1.1.3 dated 2009-11-13

 DESCRIPTION               |    6 +++---
 man/concordance.index.Rd  |    2 +-
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Package seewave updated to version 1.5.6 with previous version 1.5.5 dated 2009-06-26

Author: Jerome Sueur , Thierry Aubin , Caroline Simonis
Title: Time wave analysis and graphical representation
Description: seewave provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.

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Package rioja updated to version 0.5-6 with previous version 0.5-5 dated 2009-10-28

Author: Steve Juggins
Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer functions, and stratigraphic diagrams.

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Package pixmap updated to version 0.4-10 with previous version 0.4-9 dated 2008-07-04

Author: Roger Bivand, Friedrich Leisch and Martin Maechler
Title: Bitmap Images (``Pixel Maps'')
Description: Functions for import, export, plotting and other manipulations of bitmapped images.

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Package pgirmess updated to version 1.4.2 with previous version 1.4.1 dated 2009-11-08

Author: Patrick Giraudoux
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of ecological and spatial data

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Package msm updated to version 0.9.4 with previous version 0.9.3 dated 2009-08-26

Author: Christopher Jackson
Title: Multi-state Markov and hidden Markov models in continuous time
Description: Functions for fitting general continuous-time Markov and hidden Markov multi-state models to longitudinal data. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates. A variety of observation schemes are supported, including processes observed at arbitrary times, completely-observed processes, and censored states.

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Package matrixStats updated to version 0.1.8 with previous version 0.1.6 dated 2009-06-18

Author: Henrik Bengtsson (partly by Robert Gentleman)
Title: Methods that apply to rows and columns of a matrix
Description: This packages provides methods operating on rows and columns of matrices. The methods are optimized for speed and memory. This package is currently in a beta phase. Make sure to read the 'Roadmap' section in the package help.

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Package corcounts updated to version 1.4 with previous version 1.3 dated 2009-10-09

Author: Vinzenz Erhardt
Title: Generate correlated count random variables
Description: Generate high-dimensional correlated count random variables with a prespecified Pearson correlation.

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New package HistData with initial version 0.6-4
Package: HistData
Type: Package
Title: Data sets from the history of statistics and data visualization
Version: 0.6-4
Date: 2009-11-11
Author: Michael Friendly, with contributions by Stephane Dray, Hadley Wickham
Maintainer: Michael Friendly
Description: The HistData package provides a collection of small data sets that are interesting and important in the history of statistics and data visualization. The goal of the package is to make these available, both for instructional use and for historical research. Some of these present interesting challenges for graphics or analysis in R.
Suggests: gtools, KernSmooth, maps, ggplot2, proto, grid, reshape, plyr, lattice, ReadImages, car
License: GPL
LazyLoad: yes
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: histdata
Repository/R-Forge/Revision: 16
Date/Publication: 2009-11-13 14:58:29
Packaged: 2009-11-11 21:05:41 UTC; rforge

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Package vbmp updated to version 1.14.0 with previous version 1.12.0 dated 2009-05-10

Author: Nicola Lama , Mark Girolami
Title: Variational Bayesian Multinomial Probit Regression
Description: Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.

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Package twitteR updated to version 0.1.3 with previous version 0.1.2 dated 2009-10-20

Author: Jeff Gentry
Title: R based Twitter client
Description: Provides an interface to the Twitter web API

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Package qvalue updated to version 1.20.0 with previous version 1.18.0 dated 2009-05-10

Author: Alan Dabney and John D. Storey , with assistance from Gregory R. Warnes
Title: Q-value estimation for false discovery rate control
Description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

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Package pamr updated to version 1.44.0 with previous version 1.42.0 dated 2009-05-10

Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Title: Pam: prediction analysis for microarrays
Description: Some functions for sample classification in microarrays

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Package mvbutils updated to version 2.5.0 with previous version 2.2.0 dated 2008-11-06

Author: Mark V. Bravington
Title: Workspace organization, code and documentation editing, package prep and editing, etc.
Description: Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.

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Package multtest updated to version 2.2.0 with previous version 2.1.3 dated 2009-10-22

Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

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Package maanova updated to version 1.16.0 with previous version 1.14.0 dated 2009-05-10

Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui.
Title: Tools for analyzing Micro Array experiments
Description: Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree.

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Package kml updated to version 1.0 with previous version 0.9.2 dated 2009-02-19

Author: Christophe Genolini
Title: K-Means for Longitudinal Data (KmL)
Description: KmL is an implementation of k-means specificaly design to deal with longitudinal data. It provide facilities to deal with missing value and propose a graphical interphace for chosing the correct number of clusters.

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Package integrOmics updated to version 2.5 with previous version 2.4 dated 2009-09-23

Author: Sebastien Dejean, Ignacio Gonzalez and Kim-Anh Le Cao
Title: Integrate Omics data project
Description: The package supplies two efficients methodologies: regularized CCA and sparse PLS to unravel relationships between two heterogeneous data sets of size (nxp) and (nxq) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, integrOmics can also be applied to any other large data sets where p+q>>n. rCCA is a regularized version of CCA to deal with the large number of variables. sPLS allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results.

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Package impute updated to version 1.20.0 with previous version 1.18.0 dated 2009-09-22

Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu
Title: impute: Imputation for microarray data
Description: Imputation for microarray data (currently KNN only)

Diff between impute versions 1.18.0 dated 2009-09-22 and 1.20.0 dated 2009-11-13

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Package hopach updated to version 2.6.0 with previous version 2.4.0 dated 2009-05-10

Author: Katherine S. Pollard, with Mark J. van der Laan and Greg Wall
Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Description: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

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Package hexbin updated to version 1.20.0 with previous version 1.18.0 dated 2009-05-10

Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.

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Package grpreg updated to version 1.1 with previous version 1.0 dated 2008-11-24

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

Diff between grpreg versions 1.0 dated 2008-11-24 and 1.1 dated 2009-11-13

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Package graph updated to version 1.24.1 with previous version 1.22.2 dated 2009-05-10

Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Title: graph: A package to handle graph data structures
Description: A package that implements some simple graph handling capabilities.

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Package gpls updated to version 1.18.0 with previous version 1.16.0 dated 2009-05-10

Author: Beiying Ding
Title: Classification using generalized partial least squares
Description: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.

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Package gene2pathway updated to version 1.4.0 with previous version 1.2.0 dated 2009-05-10

Author: Holger Froehlich , contributions by Tim Beissbarth
Title: Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures
Description: The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.

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Package gWidgetsWWW updated to version 0.0-13 with previous version 0.0-12 dated 2009-11-01

Author: John Verzani
Title: Toolkit implementation of the gWidgets API for use with web pages
Description: Port of the gWidgets API to www using a local server or RApache (http://biostat.mc.vanderbilt.edu/rapache/index.html) to link R with a web page, The Ext JavaScript libararies are used to create and manipulate widgets. (www.extjs.com)

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Package debug updated to version 1.2.1 with previous version 1.2.0 dated 2008-10-27

Author: Mark V. Bravington
Title: MVB's debugger for R
Description: Debugger for R functions, with code display, graceful error recovery, line-numbered conditional breakpoints, access to exit code, flow control, and full keyboard input.

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New package Sleuth2 with initial version 1.0-0
Package: Sleuth2
Title: Data sets from Ramsey and Schafer's "Statistical Sleuth (2nd ed)"
Version: 1.0-0
Date: 2009-11-12
Author: Original by F.L. Ramsey and D.W. Schafer, modifications by Daniel W Schafer, Jeannie Sifneos and Berwin A Turlach
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)" Duxbury.
Maintainer: Berwin A Turlach
LazyData: yes
Depends: R (>= 2.6.0)
License: GPL (>= 2)
URL: http://r-forge.r-project.org/projects/sleuth2/
Repository: CRAN
Repository/R-Forge/Project: sleuth2
Repository/R-Forge/Revision: 13
Date/Publication: 2009-11-13 10:42:46
Packaged: 2009-11-12 21:04:56 UTC; rforge

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Package RLMM updated to version 1.8.0 with previous version 1.6.0 dated 2009-05-10

Author: Nusrat Rabbee , Gary Wong
Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays
Description: A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

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Package RBGL updated to version 1.22.0 with previous version 1.20.0 dated 2009-05-10

Author: Vince Carey , Li Long , R. Gentleman
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

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Package LMGene updated to version 1.16.0 with previous version 1.14.0 dated 2009-05-10

Author: David Rocke, Geun Cheol Lee, and John Tillinghast.
Title: LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
Description: LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package.

Diff between LMGene versions 1.14.0 dated 2009-05-10 and 1.16.0 dated 2009-11-13

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Package Icens updated to version 1.18.0 with previous version 1.16.0 dated 2009-05-10

Author: R. Gentleman and Alain Vandal .
Title: NPMLE for Censored and Truncated Data
Description: Many functions for computing the NPMLE for censored and truncated data.

Diff between Icens versions 1.16.0 dated 2009-05-10 and 1.18.0 dated 2009-11-13

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Package CORREP updated to version 1.12.0 with previous version 1.10.0 dated 2009-05-10

Author: Dongxiao Zhu and Youjuan Li
Title: Multivariate Correlation Estimator and Statistical Inference Procedures.
Description: Multivariate correlation estimation and statistical inference. See package vignette.

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Thu, 12 Nov 2009

Package parcor updated to version 0.2 with previous version 0.1 dated 2009-04-29

Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression.

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Package MLDS updated to version 0.2-5 with previous version 0.2-3 dated 2009-09-29

Author: Kenneth Knoblauch and Laurence T. Maloney, based in part on C code written by Laurence T. Maloney and J. N. Yang
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived supra-threshold differences. The package contains functions that allow the user to design and run a difference scaling experiment, to fit the resulting data by maximum likelihood and test the internal validity of the estimated scale.

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Package MCMCglmm updated to version 1.13 with previous version 1.12 dated 2009-10-03

Author: Jarrod Hadfield
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models

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New package histogram with initial version 0.0-21
Package: histogram
Type: Package
Title: Construction of regular and irregular histograms with different options for automatic choice of bins
Version: 0.0-21
Date: 2009-11-12
Author: Thoralf Mildenberger, Yves Rozenholc, David Zasada.
Maintainer: Thoralf Mildenberger
Description: Automatic construction of regular and irregular histograms as described in Rozenholc/Mildenberger/Gather (2009).
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-12 13:19:30 UTC; root
Repository: CRAN
Date/Publication: 2009-11-12 16:02:07

More information about histogram at CRAN
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Package gplots updated to version 2.7.4 with previous version 2.7.3 dated 2009-10-23

Author: Gregory R. Warnes. Includes R source code and/or documentation contributed by (in alphabetical order): Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data

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Package fda updated to version 2.2.0 with previous version 2.1.3 dated 2009-10-18

Author: J. O. Ramsay , Hadley Wickham , Spencer Graves , Giles Hooker
Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book.

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Package vrmlgen updated to version 1.2 with previous version 1.1 dated 2009-10-12

Author: Enrico Glaab
Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes, parametric functions and height maps in web-formats like the Virtual Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

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Package spcosa updated to version 0.2-0 with previous version 0.1-5 dated 2009-09-09

Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means.

Diff between spcosa versions 0.1-5 dated 2009-09-09 and 0.2-0 dated 2009-11-12

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Package spatgraphs updated to version 2.30 with previous version 2.27 dated 2009-09-18

Author: Tuomas Rajala
Title: Graphs for spatial point patterns
Description: Graphs, graph visualization and graph component calculations, ment to be used as a tool in spatial point pattern analysis. See package 'spatstat' for more info about spatial point patterns.

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Package roxygen updated to version 0.1-2 with previous version 0.1 dated 2008-08-31

Author: Peter Danenberg , Manuel Eugster with contributions from Hadley Wickham
Title: Literate Programming in R
Description: A Doxygen-like in-source documentation system for Rd, collation, namespace and callgraphs.

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Package ppls updated to version 1.04 with previous version 1.03 dated 2009-01-24

Author: Nicole Kraemer Anne-Laure Boulesteix
Title: Penalized Partial Least Squares
Description: This package contains linear and nonlinear regression methods based on Partial Least Squares and Penalization Techniques.

Diff between ppls versions 1.03 dated 2009-01-24 and 1.04 dated 2009-11-12

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Package mvna updated to version 1.2 with previous version 1.1-10 dated 2009-10-14

Author: Arthur Allignol
Title: Nelson-Aalen estimator of the cumulative hazard in multistate models
Description: This package computes the Nelson-Aalen estimator of the cumulative transition hazard for multistate models.

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Package memisc updated to version 0.95-23 with previous version 0.95-22 dated 2009-10-15

Author: Martin Elff
Title: Tools for Management of Survey Data, Graphics, Programming, Statistics, and Simulation
Description: One of the aims of this package is to make life easier for useRs who deal with survey data sets. It provides an infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) SPSS and Stata files. Further, it provides functionality to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates. Also some convenience tools for graphics, programming, and simulation are provided.

Diff between memisc versions 0.95-22 dated 2009-10-15 and 0.95-23 dated 2009-11-12

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Package etm updated to version 0.4-7 with previous version 0.4-6 dated 2009-09-03

Author: Arthur Allignol
Title: Empirical Transition Matrix
Description: Matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space

Diff between etm versions 0.4-6 dated 2009-09-03 and 0.4-7 dated 2009-11-12

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Package animation updated to version 1.0-9 with previous version 1.0-8 dated 2009-11-06

Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of 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.

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Package RcmdrPlugin.qual updated to version 0.4.0 with previous version 0.3.0 dated 2009-11-01

Author: Erin Hodgess
Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the Quality control class Stat 4300

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Package RaschSampler updated to version 0.8-3 with previous version 0.8-2 dated 2009-08-19

Author: Reinhold Hatzinger, Patrick Mair, Norman Verhelst
Title: Rasch Sampler
Description: Sampling binary matrices with fixed margins

Diff between RaschSampler versions 0.8-2 dated 2009-08-19 and 0.8-3 dated 2009-11-12

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Package R2jags updated to version 0.01-27 with previous version 0.01-26 dated 2009-10-13

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

Diff between R2jags versions 0.01-26 dated 2009-10-13 and 0.01-27 dated 2009-11-12

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Package MasterBayes updated to version 2.45 with previous version 2.44 dated 2009-07-21

Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficency.

Diff between MasterBayes versions 2.44 dated 2009-07-21 and 2.45 dated 2009-11-12

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Package AICcmodavg updated to version 1.04 with previous version 1.03 dated 2009-10-22

Author: Marc J. Mazerolle . Special thanks to T. Ergon for the original idea of storing candidate models in a list.
Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). Tables are printed with delta AIC and Akaike weights. The package also includes functions to conduct model averaging (multimodel inference) for a given parameter of interest or predicted values. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with linear models ('lm' class), generalized linear models ('glm' class), linear mixed models ('lme' class), multinomial and ordinal logistic regressions ('multinom' and 'polr' classes).

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Wed, 11 Nov 2009

Package e1071 updated to version 1.5-21 with previous version 1.5-20 dated 2009-10-19

Author: Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David Meyer, and Andreas Weingessel
Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...

Diff between e1071 versions 1.5-20 dated 2009-10-19 and 1.5-21 dated 2009-11-11

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Package rgdal updated to version 0.6-21 with previous version 0.6-20 dated 2009-10-30

Author: Timothy H. Keitt , Roger Bivand , Edzer Pebesma , Barry Rowlingson
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.3.1) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package.

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Package prettyR updated to version 1.7 with previous version 1.5 dated 2009-06-18

Author: Jim Lemon , Philippe Grosjean
Title: Pretty descriptive stats.
Description: Functions for conventionally formatted descriptive stats, and to format R output as HTML.

Diff between prettyR versions 1.5 dated 2009-06-18 and 1.7 dated 2009-11-11

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Package frontier updated to version 0.996-0 with previous version 0.995-8 dated 2009-10-18

Author: Tim Coelli, Arne Henningsen
Title: Stochastic Frontier Analysis
Description: Maximum Likelihood Estimation of Stochastic Frontier Production and Cost Functions. Two specifications are available: the error components specification with time-varying efficiencies (Battese and Coelli, 1992) and a model specification in which the firm effects are directly influenced by a number of variables (Battese and Coelli, 1995).

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Package forensim updated to version 1.1-2 with previous version 1.1-1 dated 2009-10-26

Author: Hinda Haned
Title: Statistical tools for the interpretation of forensic DNA mixtures
Description: Statistical methods and simulation tools for the interpretation of forensic DNA mixtures

Diff between forensim versions 1.1-1 dated 2009-10-26 and 1.1-2 dated 2009-11-11

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Package estout updated to version 0.7-1 with previous version 0.6-1 dated 2009-08-08

Author: Felix Kaminsky , inspired by the estout package for Stata.
Title: Estimates Output
Description: The function collection stores the estimates of several models and formats it to a table of the form estimate starred and std.err. below. The default output is LaTeX but output to CSV for later editing in a spreadsheet tool is possible as well. It works for linear models (lm) and panel models from the "plm"-package (plm). The added "descsto" and "desctab" enable you to export descriptive statistics of data-frames and single variables to LaTeX and CSV.

Diff between estout versions 0.6-1 dated 2009-08-08 and 0.7-1 dated 2009-11-11

 DESCRIPTION   |    6 +-
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New package aroma.light with initial version 1.15.1
Package: aroma.light
Version: 1.15.1
Date: 2009-11-01
Title: Light-weight methods for normalization and visualization of microarray data using only basic R data types
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Depends: R.methodsS3
Suggests: R.oo, R.utils, princurve
Description: Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
License: LGPL
biocViews: Infrastructure, Microarray, OneChannel, TwoChannel, MultiChannel, Visualization, Preprocessing
URL: http://www.braju.com/R/
LazyLoad: TRUE
Packaged: 2009-11-10 15:53:10 UTC; hb
Repository: CRAN
Date/Publication: 2009-11-11 13:10:12

More information about aroma.light at CRAN
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Package KFAS updated to version 0.4.7 with previous version 0.4.6 dated 2009-10-22

Author: Jouni Helske
Title: Multivariate Kalman filter and smoother, simulation smoother and forecasting of state space models. State smoothing and approximate likelihood of exponential family state space models.
Description: Package KFAS provides functions for fast Kalman filtering, state and disturbance smoothing, forecasting and simulation of multivariate time-variant state space models. All functions can use exact diffuse initialisation when distributions of some or all elements of initial state vector are unknown. Filtering, state smoothing and simulation functions use sequential processing algorithm, which is faster than standard approach, and it also allows singularity of prediction error variance matrix. KFAS also contains function for approximation of likelihood of exponential family state space models and function for state smoothing of exponential family state space models.

Diff between KFAS versions 0.4.6 dated 2009-10-22 and 0.4.7 dated 2009-11-11

 DESCRIPTION         |   23 ++++++++++++----------
 NAMESPACE           |    2 -
 R/KFAS.R            |   54 +++++++++++++++++++++++++++++++---------------------
 man/expflik.Rd      |   38 ++++++++++++++++++++++++++++++++++++
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New package vegdata with initial version 0.1
Package: vegdata
Version: 0.1
Date: 11.2009
Title: Functions to use vegetation databases (Turboveg) for vegetation analyses in R
LazyLoad: yes
LazyData: yes
Author: Florian Jansen
Maintainer: Florian Jansen
Depends: R (>= 2.0.0), foreign
Suggests: RODBC, lattice, RMySQL, Hmisc, vegan, labdsv, akima
Description: Handling of vegetation data sets from Turboveg Databases. Taxonomic valuation for German Taxonomical Standard List.
License: GPL (>= 2)
URL: http://geobot.botanik.uni-greifswald.de/reflist
Packaged: 2009-11-10 22:57:27 UTC; jansen
Repository: CRAN
Date/Publication: 2009-11-11 07:42:44

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New package nutshell with initial version 1.0
Package: nutshell
Type: Package
Title: Data for "R in a Nutshell"
Version: 1.0
Date: 2009-10-11
Author: Joseph Adler
Maintainer: Joseph Adler
Description: This package contains data sets used as examples in the book "R in a Nutshell" from O'Reilly Media. For more information on this book, see http://oreilly.com/catalog/9780596801717/
License: file LICENSE
LazyLoad: yes
Packaged: 2009-11-11 05:07:00 UTC; josephadler
Repository: CRAN
Date/Publication: 2009-11-11 07:42:31

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Package epitools updated to version 0.5-4 with previous version 0.5-3 dated 2009-04-15

Author: Tomas Aragon
Title: Epidemiology Tools
Description: EpiTools: R Package for Epidemiologic Data and Graphics

Diff between epitools versions 0.5-3 dated 2009-04-15 and 0.5-4 dated 2009-11-11

 DESCRIPTION        |    8 ++++----
 man/as.hour.Rd     |    2 +-
 man/as.month.Rd    |    2 +-
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New package ebdbNet with initial version 1.0
Package: ebdbNet
Type: Package
Title: Empirical Bayes Estimation of Dynamic Bayesian Networks
Version: 1.0
Date: 2009-11-05
Author: Andrea Rau
Maintainer: Andrea Rau
Depends: R (>= 2.8.1)
Suggests: GeneNet
Description: This package is used to infer the adjacency matrix of a network from time course data using an empirical Bayes estimation procedure based on Dynamic Bayesian Networks.
License: GPL
URL: http://www.r-project.org
LazyLoad: yes
Packaged: Tue Nov 10 16:40:59 2009; arau
Repository: CRAN
Date/Publication: 2009-11-11 07:42:20

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Tue, 10 Nov 2009

Package rlecuyer updated to version 0.3-1 with previous version 0.2 dated 2009-01-23

Author: Hana Sevcikova , Tony Rossini
Title: R interface to RNG with multiple streams
Description: Provides an interface to the C implementation of the random number generator with multiple independent streams developed by L'Ecuyer et al (2002). The main purpose of this package is to enable the use of this random number generator in parallel R applications.

Diff between rlecuyer versions 0.2 dated 2009-01-23 and 0.3-1 dated 2009-11-10

 DESCRIPTION           |   19 +++++++++++++------
 man/SetPackageSeed.Rd |    2 +-
 src/RngWrap.c         |    4 +++-
 3 files changed, 17 insertions(+), 8 deletions(-)

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Package tractor.base updated to version 1.3.0 with previous version 1.2.0 dated 2009-08-21

Author: Jon Clayden
Title: Basic functions for the TractoR (tractography with R) bundle
Description: The tractor.base package consists of functions for working with magnetic resonance images. It can read and write image files stored in Analyze, NIfTI and DICOM formats (DICOM support is read only), generate images for use as regions of interest, and manipulate and visualise images.

Diff between tractor.base versions 1.2.0 dated 2009-08-21 and 1.3.0 dated 2009-11-10

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Package spatstat updated to version 1.17-2 with previous version 1.17-1 dated 2009-11-06

Author: Adrian Baddeley and Rolf Turner , with substantial contributions of code by Marie-Colette van Lieshout, Rasmus Waagepetersen, Kasper Klitgaard Berthelsen and Dominic Schuhmacher. Additional contributions by Ang Qi Wei, C. Beale, R. Bernhardt, B. Biggerstaff, R. Bivand, F. Bonneu, J. Burgos, J.B. Chen, Y.C. Chin, B. Christensen, M. de la Cruz, P.J. Diggle, S. Eglen, A. Gault, M. Genton, P. Grabarnik, C. Graf, J. Franklin, U. Hahn, M. Hering, M.B. Hansen, M. Hazelton, J. Heikkinen, K. Hornik, R. Ihaka, R. John-Chandran, D. Johnson, J. Laake, R. Mark, J. Mateu, P. McCullagh, S. Meyer, X.C. Mi, J. Moller, L.S. Nielsen, F. Nunes, E. Parilov, J. Picka, M. Reiter, B.D. Ripley, B. Rowlingson, E. Rubak, J. Rudge, A. Sarkka, K. Schladitz, B.T. Scott, I.-M. Sintorn, M. Spiess, M. Stevenson, P. Surovy, B. Turlach, A. van Burgel, T. Verbeke, A. Villers, H. Wang, H. Wendrock and S. Wong.
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns. Contains functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images and tessellations. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

Diff between spatstat versions 1.17-1 dated 2009-11-06 and 1.17-2 dated 2009-11-10

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Package rjags updated to version 1.0.3-12 with previous version 1.0.3-11 dated 2009-10-11

Author: Martyn Plummer
Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library

Diff between rjags versions 1.0.3-11 dated 2009-10-11 and 1.0.3-12 dated 2009-11-10

 DESCRIPTION           |    8 ++++----
 NAMESPACE             |    3 ---
 R/unix/progress.bar.R |    8 ++++----
 3 files changed, 8 insertions(+), 11 deletions(-)

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Package irr updated to version 0.82 with previous version 0.81 dated 2009-10-26

Author: Matthias Gamer , Jim Lemon , Ian Fellows
Title: Various Coefficients of Interrater Reliability and Agreement
Description: Coefficients of Interrater Reliability and Agreement for quantitative, ordinal and nominal data: ICC, Finn-Coefficient, Robinson'A, Kendall's W, Cohen's Kappa, ...

Diff between irr versions 0.81 dated 2009-10-26 and 0.82 dated 2009-11-10

 CHANGES           |    3 +++
 DESCRIPTION       |    8 ++++----
 R/icc.R           |   12 ++++++------
 R/print.icclist.R |    2 +-
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 5 files changed, 15 insertions(+), 12 deletions(-)

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New package r4ss with initial version 1.0
Package: r4ss
Type: Package
Title: R code for Stock Synthesis
Version: 1.0
Date: 2009-11-07
Author: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, and other contributors
Maintainer: Ian Taylor
Depends: R (>= 2.8.0), tcltk
Description: Functions for reading output, plotting, exploring and manipulating input files for Richard Methot's Stock Synthesis fisheries stock assessment modeling platform.
License: MIT License
LazyLoad: yes
Packaged: 2009-11-09 22:39:36 UTC; ian
Repository: CRAN
Date/Publication: 2009-11-10 10:15:21

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Package fGarch updated to version 2110.80 with previous version 2100.79 dated 2009-09-28

Author: Diethelm Wuertz and Yohan Chalabi with contribution from Michal Miklovic, Chris Boudt, Pierre Chausse and others
Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Description: Environment for teaching "Financial Engineering and Computational Finance"

Diff between fGarch versions 2100.79 dated 2009-09-28 and 2110.80 dated 2009-11-10

 ChangeLog           | 2620 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 DESCRIPTION         |   10 
 R/methods-predict.R |   18 
 3 files changed, 2544 insertions(+), 104 deletions(-)

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Package Rcpp updated to version 0.6.8 with previous version 0.6.7 dated 2009-11-08

Author: Dirk Eddelbuettel with contributions by Simon Urbanek and David Reiss
Title: Rcpp R/C++ interface package
Description: R/C++ interface classes and examples The Rcpp library maps data types betweeen R and C++, and includes support for R types real, integer, character, vector, matrix, Date, datetime (i.e. POSIXct) at microsecond resolution, data frame, and function. It also supports calling R functions from C++. Several examples are included.

Diff between Rcpp versions 0.6.7 dated 2009-11-08 and 0.6.8 dated 2009-11-10

 DESCRIPTION          |    8 -
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Package CausalGAM updated to version 0.1-2 with previous version 0.1-1 dated 2009-11-08

Author: Adam Glynn , Kevin Quinn
Title: Estimation of Causal Effects with Generalized Additive Models
Description: This package implements various estimators for average treatment effects---an inverse probability weighted (IPW) estimator, an augmented inverse probability weighted (AIPW) estimator, and a standard regression estimator---that make use of generalized additive models for the treatment assignment model and/or outcome model.

Diff between CausalGAM versions 0.1-1 dated 2009-11-08 and 0.1-2 dated 2009-11-10

 DESCRIPTION |    8 ++++----
 HISTORY     |    2 +-
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 3 files changed, 6 insertions(+), 9 deletions(-)

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Mon, 09 Nov 2009

Package caret updated to version 4.30 with previous version 4.27 dated 2009-11-05

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

Diff between caret versions 4.27 dated 2009-11-05 and 4.30 dated 2009-11-09

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New package stringr with initial version 0.1.10
Package: stringr
Type: Package
Title: Make it easier to work with strings.
Version: 0.1.10
Author: Hadley Wickham
Maintainer: Hadley Wickham
Description: stringr is a set of simple wrappers that make R's string functions more consistent, simpler and easier to use. It does this by ensuring that: function and argument names (and positions) are consistent, all functions deal with NA's and zero length character appropriately, and the output data structures from each function matches the input data structures of other functions.
Depends: plyr
License: GPL-2
Collate: 'basics.r' 'regexp.r' 'match.r'
Packaged: 2009-11-09 14:43:37 UTC; hadley
Repository: CRAN
Date/Publication: 2009-11-09 15:57:09

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Package speff2trial updated to version 1.0.1 with previous version 1.0.0 dated 2009-07-02

Author: Michal Juraska , with contributions from Peter B. Gilbert , Min Zhang , Marie Davidian , Anastasios A. Tsiatis and Xiaomin Lu
Title: Semiparametric efficient estimation for a two-sample treatment effect
Description: The package performs estimation and testing of the treatment effect in a 2-group randomized clinical trial with a quantitative, dichotomous, or right-censored time-to-event endpoint. The method improves efficiency by leveraging baseline predictors of the endpoint. The inverse probability weighting technique of Robins, Rotnitzky, and Zhao (JASA, 1994) is used to provide unbiased estimation when the endpoint is missing at random.

Diff between speff2trial versions 1.0.0 dated 2009-07-02 and 1.0.1 dated 2009-11-09

 DESCRIPTION                 |   21 
 NAMESPACE                   |    7 
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Package rainbow updated to version 1.6 with previous version 1.5 dated 2009-10-08

Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, bagplots and boxplots for functional data
Description: Functions and datasets for functional data display and outlier detection.

Diff between rainbow versions 1.5 dated 2009-10-08 and 1.6 dated 2009-11-09

 CHANGELOG       |    2 ++
 DESCRIPTION     |    8 ++++----
 NAMESPACE       |    3 ++-
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Package earth updated to version 2.4-0 with previous version 2.3-5 dated 2009-10-09

Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and Rob Tibshirani.
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.)

Diff between earth versions 2.3-5 dated 2009-10-09 and 2.4-0 dated 2009-11-09

 DESCRIPTION                         |    6 
 NEWS                                |    6 
 R/earth.R                           |    2 
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Package depmix updated to version 0.9.7 with previous version 0.9.6 dated 2009-07-18

Author: Ingmar Visser
Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed categorical and continuous (timeseries) data

Diff between depmix versions 0.9.6 dated 2009-07-18 and 0.9.7 dated 2009-11-09

 CHANGES           |    6 ++++++
 DESCRIPTION       |   10 +++++-----
 README            |    4 ++--
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 4 files changed, 14 insertions(+), 8 deletions(-)

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New package Rhh with initial version 1.0
Package: Rhh
Type: Package
Title: Calculating multilocus heterozygosity and heterozygosity-heterozygosity correlation
Version: 1.0
Date: 2009-11-09
Author: Jussi Alho, Kaisa Välimäki
Maintainer: Jussi Alho
Description: This package includes functions to estimate heterozygosity-heterozygosity correlation and to calculate three estimates of individual multilocus heterozygosity: homozygosity by loci, internal relatedness, and standardized heterozygosity.
License: GPL-3
URL: http://www.helsinki.fi/biosci/egru/research/software
Encoding: latin1
Packaged: Mon Nov 9 13:01:33 2009; jalho
Repository: CRAN
Date/Publication: 2009-11-09 15:57:04

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Package ORIClust updated to version 1.0-1 with previous version 1.0-0 dated 2009-09-18

Author: Tianqing Liu, Nan Lin, Ningzhong Shi and Baoxue Zhang
Title: Order-restricted Information Criterion-based Clustering Algorithm
Description: ORIClust is a user-friendly R-based software package for gene clustering. Clusters are given by genes matched to prespecified profiles across various ordered treatment groups. It is particularly useful for analyzing data obtained from short time-course or dose-response microarray experiments.

Diff between ORIClust versions 1.0-0 dated 2009-09-18 and 1.0-1 dated 2009-11-09

 DESCRIPTION             |    6 +++---
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New package MNM with initial version 0.95-0
Package: MNM
Type: Package
Title: Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks
Version: 0.95-0
Date: 2009-11-09
Author: Klaus Nordhausen, Jyrki Mottonen, Hannu Oja
Maintainer: Klaus Nordhausen
Depends: R (>= 2.9.2), ellipse, ICS, ICSNP, SpatialNP, mvtnorm, survey
Suggests: Flury, gamlss
Description: The package provides multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components.
License: GPL (>= 2)
LazyLoad: yes
Encoding: latin1
Packaged: 2009-11-09 04:21:16 UTC; kn66583
Repository: CRAN
Date/Publication: 2009-11-09 15:40:00

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Package ICSNP updated to version 1.0-6 with previous version 1.0-5 dated 2009-09-12

Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape

Diff between ICSNP versions 1.0-5 dated 2009-09-12 and 1.0-6 dated 2009-11-09

 DESCRIPTION          |    8 ++++----
 NAMESPACE            |    2 +-
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Package GLDEX updated to version 1.0.3.4 with previous version 1.0.3.3 dated 2009-11-01

Author: Steve Su
Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Discretised and Maximum Likelihood Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood estimation. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.

Diff between GLDEX versions 1.0.3.3 dated 2009-11-01 and 1.0.3.4 dated 2009-11-09

 DESCRIPTION          |    8 +++----
 R/qqplot.gld.R       |   31 +++++++++++++++++------------
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 4 files changed, 58 insertions(+), 38 deletions(-)

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Package spls updated to version 2.1-0 with previous version 1.1-0 dated 2009-05-20

Author: Dongjun Chung , Hyonho Chun , Sunduz Keles
Title: Sparse Partial Least Squares (SPLS) Regression and Classification
Description: This package provides functions for fitting a Sparse Partial Least Squares Regression and Classification

Diff between spls versions 1.1-0 dated 2009-05-20 and 2.1-0 dated 2009-11-09

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More information about spls at CRAN
Permanent link

Sun, 08 Nov 2009

Package chron updated to version 2.3-33 with previous version 2.3-32 dated 2009-10-04

Author: S original by David James , R port by Kurt Hornik .
Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times

Diff between chron versions 2.3-32 dated 2009-10-04 and 2.3-33 dated 2009-11-08

 ChangeLog   |   11 +++++++++++
 DESCRIPTION |    8 ++++----
 NAMESPACE   |    3 +++
 R/chron.R   |    3 +++
 R/dates.R   |    4 ++++
 R/times.R   |    4 ++++
 6 files changed, 29 insertions(+), 4 deletions(-)

More information about chron at CRAN
Permanent link

Package R2WinBUGS updated to version 2.1-16 with previous version 2.1-15 dated 2009-11-05

Author: originally written by Andrew Gelman ; changes and packaged by Sibylle Sturtz and Uwe Ligges . With considerable contributions by Gregor Gorjanc and Jouni Kerman . Ported to S-PLUS by Insightful Corp.
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Description: Using this package, it is possible to call a BUGS model, summarize inferences and convergence in a table and graph, and save the simulations in arrays for easy access in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation functionality is not yet available.

Diff between R2WinBUGS versions 2.1-15 dated 2009-11-05 and 2.1-16 dated 2009-11-08

 DESCRIPTION            |    8 ++++----
 R/bugs.R               |    2 +-
 R/write.model.R        |   46 ++++++++++++++++++++++++++++++++++++----------
 inst/NEWS              |    3 +++
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 6 files changed, 51 insertions(+), 20 deletions(-)

More information about R2WinBUGS at CRAN
Permanent link

Package xtable updated to version 1.5-6 with previous version 1.5-5 dated 2009-03-24

Author: David B. Dahl
Title: Export tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables

Diff between xtable versions 1.5-5 dated 2009-03-24 and 1.5-6 dated 2009-11-08

 DESCRIPTION                |    8 ++++----
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 4 files changed, 19 insertions(+), 10 deletions(-)

More information about xtable at CRAN
Permanent link

Package pgirmess updated to version 1.4.1 with previous version 1.4.0 dated 2009-09-13

Author: Patrick Giraudoux
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of ecological and spatial data

Diff between pgirmess versions 1.4.0 dated 2009-09-13 and 1.4.1 dated 2009-11-08

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More information about pgirmess at CRAN
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Package grImport updated to version 0.4-5 with previous version 0.4-4 dated 2009-09-18

Author: Paul Murrell and Richard Walton.
Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing PostScript pictures in R plots.

Diff between grImport versions 0.4-4 dated 2009-09-18 and 0.4-5 dated 2009-11-08

 DESCRIPTION                |    6 
 R/PostScript2RGML.R        |   11 
 inst/doc/import.pdf        | 2291 ++++++++++++++++++++++-----------------------
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 5 files changed, 1168 insertions(+), 1156 deletions(-)

More information about grImport at CRAN
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Package chemometrics updated to version 0.5 with previous version 0.4 dated 2008-11-13

Author: P. Filzmoser and K. Varmuza
Title: Multivariate Statistical Analysis in Chemometrics
Description: This package is the R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)

Diff between chemometrics versions 0.4 dated 2008-11-13 and 0.5 dated 2009-11-08

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More information about chemometrics at CRAN
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Package Rcpp updated to version 0.6.7 with previous version 0.6.6 dated 2009-08-04

Author: Dirk Eddelbuettel with contributions by Simon Urbanek and David Reiss
Title: Rcpp R/C++ interface package
Description: R/C++ interface classes and examples The Rcpp library maps data types betweeen R and C++, and includes support for R types real, integer, character, vector, matrix, Date, datetime (i.e. POSIXct) at microsecond resolution, data frame, and function. It also supports calling R functions from C++. Several examples are included.

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Package tlemix updated to version 0.0.7 with previous version 0.0.6 dated 2009-07-02

Author: P. Neytchev, P. Filzmoser, R. Patnaik, A. Eisl and R. Boubela
Title: Trimmed Maximum Likelihood Estimation
Description: TLE implements a general framework for robust fitting of finite mixture models. Parameter estimation is performed using the EM algorithm.

Diff between tlemix versions 0.0.6 dated 2009-07-02 and 0.0.7 dated 2009-11-08

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Package prabclus updated to version 2.1-4 with previous version 2.1-3 dated 2009-05-06

Author: Christian Hennig , Bernhard Hausdorf
Title: Functions for clustering of presence-absence and abundance data
Description: Distance-based parametric bootstrap tests for clustering, mainly intended for presence-absence data and abundance data (clustering of species distribution ranges). Jaccard, Kulczynski, quantitative Kulczynski and geco distance measures, clustering of presence-absence and abundance data, and nearest neighbor based noise detection (R port of Byers and Raftery's (1998) "NNclean"). Main functions are prabtest, abundtest (for testing), prabclust (for clustering), prabinit (for preparing the data) and NNclean (for noise detection). The help-pages for prabtest, abundtest and prabclust contain simple standard executions. Note that the use of the package mclust (called by function prabclust) is protected by a special license, see http://www.stat.washington.edu/mclust/license.txt, particularly point 6.

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Package cem updated to version 1.0.128 with previous version 1.0.127 dated 2009-11-04

Author: Stefano Iacus Gary King Giuseppe Porro
Title: CEM: Software for Coarsened Exact Matching
Description: This program implements the coarsened exact matching algorithm (and many extensions) described in Stefano M. Iacus, Gary King, and Giuseppe Porro, "Causal Inference Without Balance Checking: Coarsened Exact Matching," http://gking.harvard.edu/files/abs/cem-plus-abs.shtml

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Package caroline updated to version 0.1-6 with previous version 0.1-3 dated 2009-10-28

Author: David M. Schruth
Title: Generic Functions for R
Description: The caroline package is a collection of generic functions useful for various applications.

Diff between caroline versions 0.1-3 dated 2009-10-28 and 0.1-6 dated 2009-11-08

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Package RFreak updated to version 0.2-6 with previous version 0.2-5 dated 2009-01-27

Author: Robin Nunkesser
Title: R/FrEAK interface
Description: An R interface to a modified version of the Free Evolutionary Algorithm Kit FrEAK. FrEAK is a toolkit written in Java to design and analyze evolutionary algorithms. Both the R interface and an extended version of FrEAK are contained in the RFreak package. For more information on FrEAK see http://sourceforge.net/projects/freak427/.

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New package CausalGAM with initial version 0.1-1
Package: CausalGAM
Version: 0.1-1
Date: 2009-10-19
Title: Estimation of Causal Effects with Generalized Additive Models
Author: Adam Glynn , Kevin Quinn
Maintainer: Kevin Quinn
Depends: R (>= 2.9.0), gam (>= 1.0.1)
Description: This package implements various estimators for average treatment effects---an inverse probability weighted (IPW) estimator, an augmented inverse probability weighted (AIPW) estimator, and a standard regression estimator---that make use of generalized additive models for the treatment assignment model and/or outcome model.
License: GPL-2
Packaged: 2009-11-07 19:49:27 UTC; kquinn
Repository: CRAN
Date/Publication: 2009-11-08 10:24:09

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New package MortalitySmooth with initial version 1.0
Package: MortalitySmooth
Type: Package
Title: Smoothing Poisson counts with P-splines
Version: 1.0
Date: 2009-11-06
Author: Carlo G Camarda
Maintainer: Carlo G Camarda
Depends: R (>= 2.7.0), svcm
Description: Smoothing one- and two-dimensional Poisson counts with P-splines specifically tailored to mortality data. Extra-Poisson variation can be accounted. Collection of mortality data and a specific function for selecting those data by country, sex, age and years.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2009-11-06 18:26:20 UTC; giancarlo
Repository: CRAN
Date/Publication: 2009-11-08 10:24:14

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Fri, 06 Nov 2009

New package topicmodels with initial version 0.0-3
Package: topicmodels
Type: Package
Title: Topic models
Version: 0.0-3
Date: 2009-11-06
Author: Bettina Gruen and Kurt Hornik
Maintainer: Bettina Gruen
Description: Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan.
Depends: stats4, methods, modeltools, tm (>= 0.4)
Suggests: clue, igraph, lasso2, OAIHarvester
SystemRequirements: Gnu Scientific Library version >= 1.8
License: GPL-2
Encoding: UTF-8
LazyLoad: yes
Packaged: 2009-11-06 15:55:32 UTC; gruen
Repository: CRAN
Date/Publication: 2009-11-06 17:09:52

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Package segmented updated to version 0.2-6 with previous version 0.2-5 dated 2009-10-26

Author: Vito M.R. Muggeo
Title: Segmented relationships in regression models
Description: Given a (generalized) linear model, segmented `updates' the model by adding one or more segmented relationships. Several variables with multiple breakpoints are allowed.

Diff between segmented versions 0.2-5 dated 2009-10-26 and 0.2-6 dated 2009-11-06

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Package rattle updated to version 2.5.3 with previous version 2.5.2 dated 2009-11-04

Author: Graham Williams
Title: A graphical user interface for data mining in R using GTK
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 and so available to the user as a script file or as an aide to the user to interact directly with 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.

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Package mstate updated to version 0.2.3 with previous version 0.2.2 dated 2009-09-24

Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco
Title: Data preparation, estimation and prediction in multi-state models
Description: Functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models

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Package flexclust updated to version 1.2-2 with previous version 1.2-1 dated 2009-07-02

Author: Friedrich Leisch, with contributions by Evgenia Dimitriadou.
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

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Package animation updated to version 1.0-8 with previous version 1.0-7 dated 2009-11-02

Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of 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.

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Package WriteXLS updated to version 1.8.3 with previous version 1.8.2 dated 2009-10-12

Author: Marc Schwartz
Title: Cross-platform Perl based R function to create Excel 2003 (XLS) files
Description: Cross-platform perl based R function to create Excel (XLS) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.

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Package StatDA updated to version 1.2 with previous version 1.1 dated 2009-01-26

Author: Peter Filzmoser and Barbara Steiger
Title: Statistical Analysis for Environmantel Data
Description: This package offers different possibilities to make statistical analysis for Environmental Data.

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Package sets updated to version 1.0-1 with previous version 1.0 dated 2009-08-04

Author: David Meyer and Kurt Hornik (with contributions by Christian Buchta)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.

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Package spatstat updated to version 1.17-1 with previous version 1.17-0 dated 2009-10-22

Author: Adrian Baddeley and Rolf Turner , with substantial contributions of code by Marie-Colette van Lieshout, Rasmus Waagepetersen, Kasper Klitgaard Berthelsen and Dominic Schuhmacher. Additional contributions by Ang Qi Wei, C. Beale, R. Bernhardt, B. Biggerstaff, R. Bivand, F. Bonneu, J. Burgos, J.B. Chen, Y.C. Chin, B. Christensen, M. de la Cruz, P.J. Diggle, S. Eglen, A. Gault, M. Genton, P. Grabarnik, C. Graf, J. Franklin, U. Hahn, M. Hering, M.B. Hansen, M. Hazelton, J. Heikkinen, K. Hornik, R. Ihaka, R. John-Chandran, D. Johnson, J. Laake, R. Mark, J. Mateu, P. McCullagh, S. Meyer, X.C. Mi, J. Moller, L.S. Nielsen, F. Nunes, E. Parilov, J. Picka, M. Reiter, B.D. Ripley, B. Rowlingson, E. Rubak, J. Rudge, A. Sarkka, K. Schladitz, B.T. Scott, I.-M. Sintorn, M. Spiess, M. Stevenson, P. Surovy, B. Turlach, A. van Burgel, T. Verbeke, A. Villers, H. Wang, H. Wendrock and S. Wong.
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Contains functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, and pixel images. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

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Package qpcR updated to version 1.2-3 with previous version 1.2-2 dated 2009-09-21

Author: Andrej-Nikolai Spiess , Christian Ritz
Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

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Package mlegp updated to version 3.1.0 with previous version 2.2.6 dated 2009-03-08

Author: Garrett M. Dancik
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots and sensitivity analysis.

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New package cusp with initial version 2.2
Package: cusp
Type: Package
Title: Cusp Catastrophe Model Fitting Using Maximum Likelihood
Version: 2.2
Date: 2009-11-05
Author: Raoul P. P. P. Grasman
Maintainer: Raoul Grasman
Suggests: onion
Description: Package for cusp catastrophe modeling using Cobb's maximum likelihood method. Contains several utility functions for plotting, and for comparing the model to linear regression and logistic curve models.
License: GPL-2
Packaged: 2009-11-05 20:24:35 UTC; zeileis
Repository: CRAN
Date/Publication: 2009-11-06 10:17:54

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Package RcppTemplate updated to version 6.1 with previous version 6.0 dated 2009-11-03

Author: Dominick Samperi
Title: Rcpp R/C++ Object Mapping Library and Package Template
Description: The Rcpp class library enables C++ to speak the language of R. The library maps the most commonly used R data structures to C++ classes. This includes vectors, matrices, factors, dates, data frames, time series, and functions. R can call C++ functions, and C++ objects can call R functions, and the parameters and return values can be of any of the types just mentioned. This package serves two roles: 1. it serves as a demo package for Rcpp, and 2. it serves as a template for the creation of new packages that use the Rcpp library (and also for packages that do not). An important goal of the library is to support the creation of high-performance packages that do heavy computations on large data sets where a hybrid R/C++ strategy is the best fit. See the document RcppDoc.pdf for more information. The R package Rcpp is a forked version of a previous version of this software and is not discussed here.

Diff between RcppTemplate versions 6.0 dated 2009-11-03 and 6.1 dated 2009-11-06

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Package Rassoc updated to version 1.01 with previous version 1.0 dated 2009-07-30

Author: Yong ZANG , Wingkam FUNG , Gang ZHENG
Title: Robust tests for case-control genetic association studies
Description: This package supplies several robust tests for case-control genetic association studies. The tests contained in this package are: allelic based test, Cochran-Armitage trend test, maximin efficiency robust test, MAX3 test and genetic model selection test. For each test, the corresponding R code reports the test statistics and the associated p-value.

Diff between Rassoc versions 1.0 dated 2009-07-30 and 1.01 dated 2009-11-06

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New package Bolstad2 with initial version 1.0-20
Package: Bolstad2
Version: 1.0-20
Date: 2009-11-06
Title: Bolstad functions
Author: James Curran
Maintainer: James M. Curran
Description: A set of R functions and data sets for the book Understanding Computational Bayesian Statistics, Bolstad, W.M. (2009), John Wiley & Sons ISBN xxx
License: GPL (>= 2)
URL: http://www.waikato.ac.nz/Staff/bolstad
Packaged: 2009-11-06 07:09:44 UTC; curran
Repository: CRAN
Date/Publication: 2009-11-06 10:17:32

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Thu, 05 Nov 2009

Package spdep updated to version 0.4-52 with previous version 0.4-50 dated 2009-10-19

Author: Roger Bivand , with contributions by Luc Anselin, Renato Assunção, Olaf Berke, Andrew Bernat, Marilia Carvalho, Yongwan Chun, Bjarke Christensen, Carsten Dormann, Stéphane Dray, Rein Halbersma, Elias Krainski, Nicholas Lewin-Koh, Hongfei Li, Jielai Ma, Giovanni Millo, Werner Mueller, Hisaji Ono, Pedro Peres-Neto, Markus Reder, Michael Tiefelsdorf, and Danlin Yu.
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tesselations, for summarising these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.

Diff between spdep versions 0.4-50 dated 2009-10-19 and 0.4-52 dated 2009-11-05

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New package dclone with initial version 0.9-0
Package: dclone
Type: Package
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Version: 0.9-0
Date: 2009-10-19
Author: Peter Solymos
Maintainer: Peter Solymos
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.
License: GPL-2
Depends: R (>= 2.7.0), rjags, coda (>= 0.13), R2WinBUGS, mvnormtest
Imports: stats
SystemRequirements: jags (== 1.0.3), WinBUGS (== 1.4)
URL: https://r-forge.r-project.org/projects/dcr/
LazyLoad: yes
LazyData: true
Repository: CRAN
Repository/R-Forge/Project: dcr
Repository/R-Forge/Revision: 52
Date/Publication: 2009-11-05 20:29:10
Packaged: 2009-11-04 21:09:50 UTC; rforge

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Package bipartite updated to version 1.03 with previous version 1.02 dated 2009-09-12

Author: Carsten F. Dormann and Bernd Gruber, with additional code from Mariano Devoto, Jochen Fruend, Jose Iriondo and Diego Vazquez, also based on C-code developed by Nils Bluethgen and by Miguel Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological indices.
Description: Bipartite provides functions to viualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focusses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.

Diff between bipartite versions 1.02 dated 2009-09-12 and 1.03 dated 2009-11-05

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New package adephylo with initial version 1.0-1
Package: adephylo
Version: 1.0-1
Date: 2009/11/5
Title: adephylo: exploratory analyses for the phylogenetic comparative method.
Author: Thibaut Jombart , Stephane Dray
Maintainer: Thibaut Jombart
Suggests:
Depends: methods, phylobase, ape, ade4
Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
License: GPL (>= 2)
LazyLoad: yes
Collate: utils.R partition.R table.phylo4d.R distances.R proximities.R orthobasis.R ppca.R orthogram.R abouheif.R moran.R zzz.R
Packaged: 2009-11-05 18:13:06 UTC; thibaut
Repository: CRAN
Date/Publication: 2009-11-05 20:05:18

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Package SimComp updated to version 1.4.3 with previous version 1.4.2 dated 2009-10-22

Author: Mario Hasler
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). The procedure of Hasler (2009) is applied for differences or ratios of means. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous covariance matrices.

Diff between SimComp versions 1.4.2 dated 2009-10-22 and 1.4.3 dated 2009-11-05

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New package SDisc with initial version 1.17
Package: SDisc
Type: Package
Title: Integrated methodology for the identification of homogeneous profiles in data distribution
Version: 1.17
Date: 2009-10-27
Author: Fabrice Colas
Maintainer: Fabrice Colas
Description: Integrated set of tools and methods to identify homogeneous profiles/subtypes in data distribution by cluster analysis. It includes methods for data treatment and pre-processing, repeated cluster analysis, model selection, model reliability and reproducibility assessment, profiles characterization and validation by visual and table summaries. It applies particularly to the search for more homogeneous profiles in cohort studies.
Depends: R (>= 2.5.1), mclust, stats, utils, RColorBrewer, abind, xtable, digest, e1071, snow
License: BSD
URL: https://gforge.nbic.nl/projects/subtypediscover/, http://www.grano-salis.net/
Packaged: 2009-11-05 10:39:32 UTC; fcolas
Repository: CRAN
Date/Publication: 2009-11-05 19:43:24

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Package R2WinBUGS updated to version 2.1-15 with previous version 2.1-14 dated 2009-04-14

Author: originally written by Andrew Gelman ; changes and packaged by Sibylle Sturtz and Uwe Ligges . With considerable contributions by Gregor Gorjanc and Jouni Kerman . Ported to S-PLUS by Insightful Corp.
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Description: Using this package, it is possible to call a BUGS model, summarize inferences and convergence in a table and graph, and save the simulations in arrays for easy access in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation functionality is not yet available.

Diff between R2WinBUGS versions 2.1-14 dated 2009-04-14 and 2.1-15 dated 2009-11-05

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Package GeoXp updated to version 1.4 with previous version 1.3 dated 2008-10-12

Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne Ruiz-Gazen, Christine Thomas-Agnan
Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics, spatial econometrics, geography, ecology etc allowing to link dynamically statistical plots with elementary maps. This coupling consists in the fact that the selection of a zone on the map results in the automatic highlighting of the corresponding points on the statistical graph or reversely the selection of a portion of the graph results in the automatic highlighting of the corresponding points on the map. GeoXp includes tools from different areas of spatial statistics including geostatistics as well as spatial econometrics and point processes. Besides elementary plots like boxplots, histograms or simple scatterplos, GeoXp also couples with maps Moran scatterplots, variogram cloud, Lorentz Curves,...In order to make the most of the multidimensionality of the data, GeoXp includes some dimension reduction techniques such as PCA.

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Package DoE.base updated to version 0.9-7 with previous version 0.9-6 dated 2009-11-05

Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.

Diff between DoE.base versions 0.9-6 dated 2009-11-05 and 0.9-7 dated 2009-11-05

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Package DTDA updated to version 1.2-0 with previous version 1.1 dated 2009-09-21

Author: Carla Moreira, Jacobo de U\eqn{\mbox{\textasciitilde}}{~}na- \eqn{\mbox{\textasciitilde}}{'}Alvarez and Rosa Crujeiras
Title: Doubly truncated data analysis
Description: This package implements different algorithms for analyzing randomly truncated data, one-sided and two-sided (i.e. doubly) truncated data.

Diff between DTDA versions 1.1 dated 2009-09-21 and 1.2-0 dated 2009-11-05

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Package quantreg updated to version 4.44 with previous version 4.43 dated 2009-10-19

Author: Roger Koenker
Title: Quantile Regression
Description: Quantile regression and related methods.

Diff between quantreg versions 4.43 dated 2009-10-19 and 4.44 dated 2009-11-05

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Package proxy updated to version 0.4-5 with previous version 0.4-4 dated 2009-10-13

Author: David Meyer and Christian Buchta
Title: Distance and Similarity Measures
Description: Provides an extensible framework for the effcient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

Diff between proxy versions 0.4-4 dated 2009-10-13 and 0.4-5 dated 2009-11-05

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Package oce updated to version 0.1-80 with previous version 0.1-79 dated 2009-10-26

Author: Dan Kelley
Title: Analysis of Oceanographic data
Description: Supports the analysis of Oceanographic data, including ADP measurements, CTD measurements, sectional data, sea-level timeseries, 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.

Diff between oce versions 0.1-79 dated 2009-10-26 and 0.1-80 dated 2009-11-05

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Package lordif updated to version 0.1-3 with previous version 0.1-2 dated 2009-10-14

Author: Seung W. Choi, with contributions from Laura E. Gibbons and Paul K. Crane
Title: Logistic Regression Differential Item Functioning using IRT
Description: Analysis of Differential Item Functioning (DIF) for dichotomous and polytomous items using an iterative hybrid of (ordinal) logistic regression and item response theory (IRT).

Diff between lordif versions 0.1-2 dated 2009-10-14 and 0.1-3 dated 2009-11-05

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Package hash updated to version 1.0.3 with previous version 1.0.2 dated 2009-10-12

Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor.

Diff between hash versions 1.0.2 dated 2009-10-12 and 1.0.3 dated 2009-11-05

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Package ff updated to version 2.1-1 with previous version 2.1-0 dated 2009-11-03

Author: Daniel Adler , Christian Gl\xE4ser , Oleg Nenadic , Jens Oehlschl\xE4gel , Walter Zucchini
Title: memory-efficient storage of large data on disk and fast access functions
Description: The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Diff between ff versions 2.1-0 dated 2009-11-03 and 2.1-1 dated 2009-11-05

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Package equate updated to version 0.1-1 with previous version 0.1-0 dated 2009-11-01

Author: Anthony Albano
Title: Traditional Methods for Test Score Equating
Description: The equate package contains functions for traditional equating under both random groups and nonequivalent groups with anchor test designs. Mean, linear, and equipercentile equating are supported as are methods for univariate and bivariate presmoothing of score distributions.

Diff between equate versions 0.1-0 dated 2009-11-01 and 0.1-1 dated 2009-11-05

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Package caret updated to version 4.27 with previous version 4.26 dated 2009-10-28

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

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Package analogue updated to version 0.6-22 with previous version 0.6-21 dated 2009-11-03

Author: Gavin L. Simpson, Jari Oksanen
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.

Diff between analogue versions 0.6-21 dated 2009-11-03 and 0.6-22 dated 2009-11-05

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Package SparseM updated to version 0.83 with previous version 0.80 dated 2009-05-12

Author: Roger Koenker and Pin Ng
Title: Sparse Linear Algebra
Description: Basic linear algebra for sparse matrices

Diff between SparseM versions 0.80 dated 2009-05-12 and 0.83 dated 2009-11-05

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Package PCIT updated to version 1.02-1 with previous version 1.01-1 dated 2009-08-28

Author: Nathan S. Watson-Haigh
Title: PCIT algorithm - Partial Correlation Coefficient with Information Theory
Description: This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) algorithm developed by Reverter and Chan (2008). The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks.

Diff between PCIT versions 1.01-1 dated 2009-08-28 and 1.02-1 dated 2009-11-05

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New package HDMD with initial version 1.0
Package: HDMD
Type: Package
Title: Statistical Analysis Tools for High Dimension Molecular Data (HDMD)
Version: 1.0
Date: 2009-11-03
Author: Lisa McFerrin
Maintainer: Lisa McFerrin
Depends: psych, MASS, base
Suggests: scatterplot3d
Description: High Dimensional Molecular Data (HDMD) typically have many more variables or dimensions than observations or replicates (D>>N). This can cause many statistical procedures to fail, become intractable, or produce misleading results. This package provides several tools to reduce dimensionality and analyze biological data for meaningful interpretation of results. Factor Analysis (FA), Principal Components Analysis (PCA) and Discriminant Analysis (DA) are frequently used multivariate techniques. However, PCA methods \code{\link{prcomp}} and \code{\link{princomp}} do not reflect the proportion of total variation of each principal component. \code{\link{Loadings.variation}} displays the relative and cumulative contribution of variation for each component by accounting for all variability in data. When D>>N, the maximum likelihood method cannot be applied in FA and the the principal axes method must be used instead, as in \code{\link{factor.pa}} of the \code{\link{psych}} package. The \code{\link{factor.pa.ginv}} function in this package further allows for a singular covariance matrix by applying a general inverse method to estimate factor scores. Moreover, \code{\link{factor.pa.ginv}} removes and warns of any variables that are constant, which would otherwise create an invalid covariance matrix. \code{\link{Promax.only}} further allows users to define rotation parameters during factor estimation. Similar to the Euclidean distance, the Mahalanobis distance estimates the relationship among groups. \code{\link{pairwise.mahalanobis}} computes all such pairwise Mahalanobis distances among groups and is useful for quantifying the separation of groups in DA. Genetic sequences are composed of discrete alphabetic characters, which makes estimates of variability difficult. \code{\link{MolecularEntropy}} and \code{\link{MolecularMI}} calculate the entropy and mutual information to estimate variability and covariability, respectively, of DNA or Amino Acid sequences. Functional grouping of amino acids (Atchley et al 1999) is also available for entropy and mutual information estimation. Mutual information values can be normalized by \code{\link{NMI}} to account for the background distribution arising from the stochastic pairing of independent, random sites. Alternatively, discrete alphabetic sequences can be transformed into biologically informative metrics to be used in various multivariate procedures. \code{\link{FactorTransform}} converts amino acid sequences using the amino acid indices determined by Atchley et al 2005.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-04 18:18:58 UTC; Lisa
Repository: CRAN
Date/Publication: 2009-11-05 12:34:14

More information about HDMD at CRAN
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Package DoE.base updated to version 0.9-6 with previous version 0.9-5 dated 2009-11-03

Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.

Diff between DoE.base versions 0.9-5 dated 2009-11-03 and 0.9-6 dated 2009-11-05

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Package CircSpatial updated to version 1.0-1 with previous version 1.0 dated 2009-09-21

Author: Bill Morphet
Title: Functions For Circular Spatial Data
Description: The package is a collection of functions for color continuous high resolution images of circular spatial data, circular kriging, and simulation of circular random fields.

Diff between CircSpatial versions 1.0 dated 2009-09-21 and 1.0-1 dated 2009-11-05

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Wed, 04 Nov 2009

Package meta updated to version 1.1-4 with previous version 1.1-3 dated 2009-10-30

Author: Guido Schwarzer
Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.

Diff between meta versions 1.1-3 dated 2009-10-30 and 1.1-4 dated 2009-11-04

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Package mAr updated to version 1.1-2 with previous version 1.1-1 dated 2007-04-13

Author: S. M. Barbosa
Title: Multivariate AutoRegressive analysis
Description: R functions for multivariate autoregressive analysis

Diff between mAr versions 1.1-1 dated 2007-04-13 and 1.1-2 dated 2009-11-04

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Package dlnm updated to version 1.1.1 with previous version 1.1.0 dated 2009-10-19

Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and cross-basis matrices in order to run distributed lag models and their non-linear extension, then to predict and graph the results for a fitted model.

Diff between dlnm versions 1.1.0 dated 2009-10-19 and 1.1.1 dated 2009-11-04

 DESCRIPTION               |    8 
 R/crosspred.R             |    2 
 R/mkbasis.R               |    4 
 inst/ChangeLog            |    9 
 inst/doc/Rplots.pdf       |    4 
 inst/doc/dlnmOverview.pdf |  944 +++++++++++++++++++++++-----------------------
 6 files changed, 494 insertions(+), 477 deletions(-)

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Permanent link

Package YieldCurve updated to version 2.0 with previous version 1.0 dated 2009-08-04

Author: Sergio Salvino Guirreri
Title: Modelling and estimation of the yield curve
Description: Modelling the yield curve with some parametric models. The models implemented are: Nelson-Siegel, Diebold-Li and Svensson. The package also includes the data of the term structure of interest rate of Federal Reserve Bank and European Central Bank.

Diff between YieldCurve versions 1.0 dated 2009-08-04 and 2.0 dated 2009-11-04

 DESCRIPTION               |   13 +++++++------
 man/Srates.Rd             |   12 ++++++------
 man/YieldCurve-package.Rd |   10 ++++------
 3 files changed, 17 insertions(+), 18 deletions(-)

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Permanent link

New package psychotree with initial version 0.9-0
Package: psychotree
Title: Recursive Partitioning Based on Psychometric Models
Version: 0.9-0
Date: 2009-11-04
Author: Achim Zeileis, Carolin Strobl, Florian Wickelmaier
Maintainer: Achim Zeileis
Depends: R (>= 2.0.0), stats, party, strucchange
Imports: graphics, stats, sandwich
Description: Recursive partitioning based on psychometric models, employing the general MOB algorithm (from package party). Currently, only Bradley-Terry trees are implemented.
License: GPL-2
Packaged: 2009-11-04 11:29:47 UTC; zeileis
Repository: CRAN
Date/Publication: 2009-11-04 11:32:07

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Package akima updated to version 0.5-4 with previous version 0.5-3 dated 2009-09-21

Author: Fortran code by H. Akima R port by Albrecht Gebhardt aspline function by Thomas Petzoldt enhancements and corrections by Martin Maechler
Title: Interpolation of irregularly spaced data
Description: Linear or cubic spline interpolation for irregular gridded data

Diff between akima versions 0.5-3 dated 2009-09-21 and 0.5-4 dated 2009-11-04

 ChangeLog    |    8 ++++----
 DESCRIPTION  |    6 +++---
 man/akima.Rd |   23 +++++++++++------------
 3 files changed, 18 insertions(+), 19 deletions(-)

More information about akima at CRAN
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Package RobRex updated to version 0.7 with previous version 0.6.1 dated 2009-02-28

Author: Matthias Kohl
Title: Optimally robust influence curves for regression and scale
Description: functions for the determination of optimally robust influence curves in case of linear regression with unknown scale and standard normal distributed errors where the regressor is random.

Diff between RobRex versions 0.6.1 dated 2009-02-28 and 0.7 dated 2009-11-04

 DESCRIPTION            |   36 ++++++++++++++++++++--------------
 inst/NEWS              |   51 ++++++++++++++++++++++++++++++++++++++++++++++++-
 inst/TOBEDONE          |only
 inst/scripts/example.R |only
 tests                  |only
 5 files changed, 71 insertions(+), 16 deletions(-)

More information about RobRex at CRAN
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Package RobLox updated to version 0.7 with previous version 0.6.1 dated 2008-11-30

Author: Matthias Kohl
Title: Optimally robust influence curves and estimators for location and scale
Description: Functions for the determination of optimally robust influence curves and estimators in case of normal location and/or scale

Diff between RobLox versions 0.6.1 dated 2008-11-30 and 0.7 dated 2009-11-04

 DESCRIPTION                   |   36 ++--
 NAMESPACE                     |    3 
 R/colRoblox.R                 |    6 
 R/finiteSampleCorrection.R    |only
 R/rlsOptIC_TuMad.R            |    4 
 R/roblox.R                    |  363 ++++++++++++++++++++++++++++++------------
 R/rowRoblox.R                 |  205 ++++++++++++++++++++---
 R/sysdata.rda                 |binary
 inst/CITATION                 |    4 
 inst/NEWS                     |   50 +++++
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 man/roblox.Rd                 |   28 ++-
 man/rowRoblox.Rd              |   22 +-
 tests                         |only
 16 files changed, 559 insertions(+), 162 deletions(-)

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Permanent link

New package RobLoxBioC with initial version 0.7
Package: RobLoxBioC
Version: 0.7
Date: 2009-11-01
Title: Infinitesimally robust estimators for preprocessing omics data
Description: Functions for the determination of optimally robust influence curves and estimators for preprocessing omics data, in particular gene expression data.
Depends: R(>= 2.8.1), methods, Biobase, affy, beadarray, distr, RobLox, lattice, RColorBrewer
Author: Matthias Kohl
Maintainer: Matthias Kohl
LazyLoad: yes
License: LGPL-3
URL: http://robast.r-forge.r-project.org/
Encoding: latin1
LastChangedDate: {$LastChangedDate: 2009-11-01 11:53:32 +0100 (So, 01. Nov 2009) $}
LastChangedRevision: {$LastChangedRevision: 394 $}
Packaged: 2009-11-04 10:55:08 UTC; btms02
Repository: CRAN
Date/Publication: 2009-11-04 13:09:38

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Permanent link

Package RobAStBase updated to version 0.7 with previous version 0.1.5 dated 2009-01-13

Author: Matthias Kohl, Peter Ruckdeschel
Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.

Diff between RobAStBase versions 0.1.5 dated 2009-01-13 and 0.7 dated 2009-11-04

 DESCRIPTION                         |   35 -
 NAMESPACE                           |   20 
 R/AllClass.R                        |   62 +
 R/AllGeneric.R                      |   52 +
 R/AllPlot.R                         |  211 +++++-
 R/AllShow.R                         |   19 
 R/ContIC.R                          |    8 
 R/IC.R                              |   10 
 R/Neighborhood.R                    |    4 
 R/RobAStBaseOptions.R               |    7 
 R/RobModel.R                        |    7 
 R/TotalVarIC.R                      |   19 
 R/Weights.R                         |   14 
 R/bALEstimate.R                     |    8 
 R/comparePlot.R                     |  354 +++++++++-
 R/generateICfct.R                   |   18 
 R/getBiasIC.R                       |    2 
 R/getRiskIC.R                       |    1 
 R/getboundedIC.R                    |only
 R/infoPlot.R                        |  386 +++++++++--
 R/kStepEstimate.R                   |only
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 R/locMEstimator.R                   |    6 
 R/masked.R                          |only
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 R/optIC.R                           |    9 
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 inst/NEWS                           |  206 ++++++
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 man/BdStWeight-class.Rd             |    8 
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 man/ContIC-class.Rd                 |    3 
 man/ContNeighborhood-class.Rd       |    4 
 man/FixRobModel-class.Rd            |    4 
 man/HampIC-class.Rd                 |   25 
 man/HampelWeight-class.Rd           |   10 
 man/IC-class.Rd                     |   12 
 man/InfRobModel-class.Rd            |    4 
 man/InfluenceCurve-class.Rd         |    8 
 man/MEstimate-class.Rd              |   18 
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 man/RobAStBaseOptions.Rd            |   14 
 man/RobAStControl-class.Rd          |    3 
 man/RobModel-class.Rd               |   11 
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 man/TotalVarIC-class.Rd             |   30 
 man/TotalVarNeighborhood-class.Rd   |    4 
 man/UncondNeighborhood-class.Rd     |    4 
 man/comparePlot.Rd                  |  118 +++
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 man/getRiskIC.Rd                    |    2 
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 man/kStepEstimator.Rd               |  120 ++-
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 70 files changed, 2794 insertions(+), 1168 deletions(-)

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Permanent link

Package ROptRegTS updated to version 0.7 with previous version 0.6.1 dated 2009-02-28

Author: Matthias Kohl , Peter Ruckdeschel
Title: Optimally robust estimation for regression-type models
Description: Optimally robust estimation for regression-type models using S4 classes and methods

Diff between ROptRegTS versions 0.6.1 dated 2009-02-28 and 0.7 dated 2009-11-04

 DESCRIPTION                         |   34 ++++++++++++++++++++--------------
 inst/NEWS                           |   35 +++++++++++++++++++++++++++++++++++
 inst/TOBEDONE                       |only
 man/CondIC-class.Rd                 |    2 +-
 man/CondNeighborhood-class.Rd       |    2 +-
 man/FixRobRegTypeModel-class.Rd     |    2 +-
 man/InfRobRegTypeModel-class.Rd     |    2 +-
 man/RegTypeFamily-class.Rd          |    2 +-
 man/generateIC-methods.Rd           |    2 +-
 man/getAsRiskRegTS.Rd               |    2 +-
 man/getFiRiskRegTS.Rd               |    2 +-
 man/getFixClipRegTS.Rd              |    2 +-
 man/getIneffDiff-methods.Rd         |    2 +-
 man/getInfCentRegTS.Rd              |    2 +-
 man/getInfClipRegTS.Rd              |    2 +-
 man/getInfGammaRegTS.Rd             |    4 ++--
 man/getInfStandRegTS.Rd             |    2 +-
 man/leastFavorableRadius-methods.Rd |    2 +-
 man/optIC-methods.Rd                |    2 +-
 man/radiusMinimaxIC-methods.Rd      |    2 +-
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 21 files changed, 73 insertions(+), 32 deletions(-)

More information about ROptRegTS at CRAN
Permanent link

Package ROptEstOld updated to version 0.7 with previous version 0.5.2 dated 2009-02-28

Author: Matthias Kohl
Title: Optimally robust estimation - old version
Description: Optimally robust estimation using S4 classes and methods. Old version still needed for current versions of ROptRegTS and RobRex.

Diff between ROptEstOld versions 0.5.2 dated 2009-02-28 and 0.7 dated 2009-11-04

 ROptEstOld-0.5.2/ROptEstOld/R/DistrSymmList.R                 |only
 ROptEstOld-0.5.2/ROptEstOld/R/PosDefSymmMatrix.R              |only
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 ROptEstOld-0.7/ROptEstOld/DESCRIPTION                         |   33 +++---
 ROptEstOld-0.7/ROptEstOld/NAMESPACE                           |   19 ---
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 ROptEstOld-0.7/ROptEstOld/R/AllGeneric.R                      |    6 -
 ROptEstOld-0.7/ROptEstOld/R/AllShow.R                         |    7 -
 ROptEstOld-0.7/ROptEstOld/R/Symmetry.R                        |   17 ---
 ROptEstOld-0.7/ROptEstOld/inst                                |only
 ROptEstOld-0.7/ROptEstOld/man/EvenSymmetric.Rd                |    2 
 ROptEstOld-0.7/ROptEstOld/man/FunctionSymmetry-class.Rd       |    3 
 ROptEstOld-0.7/ROptEstOld/man/GammaFamily.Rd                  |    2 
 ROptEstOld-0.7/ROptEstOld/man/OddSymmetric.Rd                 |    2 
 ROptEstOld-0.7/ROptEstOld/man/TotalVarIC-class.Rd             |    3 
 ROptEstOld-0.7/ROptEstOld/man/asUnOvShoot-class.Rd            |    2 
 ROptEstOld-0.7/ROptEstOld/man/fiUnOvShoot-class.Rd            |    2 
 29 files changed, 35 insertions(+), 118 deletions(-)

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Package ROptEst updated to version 0.7 with previous version 0.6.3 dated 2009-01-13

Author: Matthias Kohl, Peter Ruckdeschel
Title: Optimally robust estimation
Description: Optimally robust estimation in general smoothly parameterized models using S4 classes and methods.

Diff between ROptEst versions 0.6.3 dated 2009-01-13 and 0.7 dated 2009-11-04

 DESCRIPTION                             |   35 
 NAMESPACE                               |    4 
 R/AllGeneric.R                          |    5 
 R/LowerCaseMultivariate.R               |   83 +
 R/cniperCont.R                          |   10 
 R/getAsRisk.R                           |   38 
 R/getFixRobIC_fiUnOvShoot.R             |    2 
 R/getIneffDiff.R                        |   43 
 R/getInfCent.R                          |   50 
 R/getInfClip.R                          |    4 
 R/getInfGamma.R                         |   28 
 R/getInfLM.R                            |only
 R/getInfRobIC_asBias.R                  |  128 +
 R/getInfRobIC_asCov.R                   |   66 
 R/getInfRobIC_asGRisk.R                 |  855 +++++++++--
 R/getInfRobIC_asHampel.R                |  557 +++++--
 R/getInfRobIC_asUnOvShoot.R             |    5 
 R/getInfStand.R                         |    2 
 R/getInfV.R                             |   28 
 R/getModifyIC.R                         |  186 +-
 R/leastFavorableRadius.R                |   61 
 R/optIC.R                               |   47 
 R/optRisk.R                             |    4 
 R/radiusMinimaxIC.R                     |   78 -
 R/roptest.R                             |   63 
 inst/NEWS                               |  188 ++
 inst/TOBEDONE                           |only
 inst/scripts/BinomialModel.R            | 2409 +++++++++++++++++++++++++++++++-
 inst/scripts/ExponentialScaleModel.R    |  203 ++
 inst/scripts/GammaModel.R               |   56 
 inst/scripts/GumbelLocationModel.R      |    2 
 inst/scripts/LognormalAndNormalModel.R  |    8 
 inst/scripts/NormalLocationScaleModel.R |   82 +
 inst/scripts/PoissonModel.R             |   15 
 man/0ROptEst-package.Rd                 |   26 
 man/getAsRisk.Rd                        |  148 +
 man/getFixRobIC.Rd                      |    3 
 man/getIneffDiff.Rd                     |   17 
 man/getInfCent.Rd                       |   19 
 man/getInfClip.Rd                       |    6 
 man/getInfGamma.Rd                      |   14 
 man/getInfRobIC.Rd                      |  119 +
 man/getInfStand.Rd                      |    6 
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 54 files changed, 5174 insertions(+), 749 deletions(-)

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Permanent link

Package trackObjs updated to version 0.8-6 with previous version 0.8-3 dated 2009-02-20

Author: Tony Plate
Title: Track Objects
Description: Stores objects in files on disk so that files are automatically rewritten when objects are changed, and so that objects are accessible but do not occupy memory until they are accessed. Also tracks times when objects are created and modified, and caches some basic characteristics of objects to allow for fast summaries of objects.

Diff between trackObjs versions 0.8-3 dated 2009-02-20 and 0.8-6 dated 2009-11-04

 trackObjs-0.8-3/trackObjs/man/trackObjs.Rd         |only
 trackObjs-0.8-6/trackObjs/DESCRIPTION              |   32 +++++++++++----------
 trackObjs-0.8-6/trackObjs/NEWS                     |    7 +++-
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 trackObjs-0.8-6/trackObjs/man/track.future.Rd      |    2 -
 trackObjs-0.8-6/trackObjs/man/track.manage.Rd      |    2 -
 trackObjs-0.8-6/trackObjs/man/track.options.Rd     |    2 -
 trackObjs-0.8-6/trackObjs/man/track.rebuild.Rd     |    2 -
 trackObjs-0.8-6/trackObjs/man/track.setup.Rd       |    2 -
 trackObjs-0.8-6/trackObjs/man/track.status.Rd      |    2 -
 trackObjs-0.8-6/trackObjs/man/track.summary.Rd     |    2 -
 trackObjs-0.8-6/trackObjs/man/trackObjs-package.Rd |only
 12 files changed, 33 insertions(+), 26 deletions(-)

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Permanent link

Package rattle updated to version 2.5.2 with previous version 2.5.1 dated 2009-10-26

Author: Graham Williams
Title: A graphical user interface for data mining in R using GTK
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 and so available to the user as a script file or as an aide to the user to interact directly with 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.

Diff between rattle versions 2.5.1 dated 2009-10-26 and 2.5.2 dated 2009-11-04

 DESCRIPTION                    |   19 ++++++------
 R/explore.R                    |   27 +++++++-----------
 R/export.R                     |   12 +++++---
 R/model.R                      |   26 +++++++++--------
 R/rattle.R                     |   17 +++--------
 R/survival.R                   |   55 ++++++++++++++++++++++++++++++++++++
 data/audit.RData               |binary
 data/weather.RData             |binary
 data/weatherCanberra.RData     |binary
 data/weatherSydney.RData       |binary
 inst/arff/weather.arff         |    4 +-
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 inst/arff/weatherSydney.arff   |   37 ++++++++++++++++++++++--
 inst/csv/weatherCanberra.csv   |   31 ++++++++++++++++++++
 inst/csv/weatherSydney.csv     |   31 ++++++++++++++++++++
 inst/etc/rattle.glade          |   61 ++++++++++++++++++++---------------------
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More information about rattle at CRAN
Permanent link

Package pmml updated to version 1.2.20 with previous version 1.2.19 dated 2009-10-26

Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Title: Generate PMML for various models
Description: The Predictive Modelling Markup Language (PMML) is a language for representing models, in an application independent way. Such models can then be loaded into other applications supporting PMML, including ADAPA from Zementis, Teradata Warehouse Miner and IBM's DB2. The package provides a generic pmml function to generate pmml for an object. Using a S3 generic function the approriate method for the class of the supplied object is dispatched. The package currently supports the export of PMML for linear regression, SVMs, rpart classification trees, randomSurvivalForest forest models, and kmeans clusters. This package is part of the Rattle toolkit.

Diff between pmml versions 1.2.19 dated 2009-10-26 and 1.2.20 dated 2009-11-04

 DESCRIPTION       |    8 ++++----
 NAMESPACE         |    1 +
 R/pmml.R          |    5 +++--
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Package mixreg updated to version 0.0-3 with previous version 0.0-2 dated 2006-09-12

Author: Rolf Turner
Title: Functions to fit mixtures of regressions.
Description: Fits mixtures of (possibly multivariate) regressions (which has been described as doing ANCOVA when you don't know the levels).

Diff between mixreg versions 0.0-2 dated 2006-09-12 and 0.0-3 dated 2009-11-04

 mixreg-0.0-2/mixreg/aphids.dat         |only
 mixreg-0.0-3/mixreg/ChangeLog          |only
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 mixreg-0.0-3/mixreg/R/boot.sam.R       |    4 ++--
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 mixreg-0.0-3/mixreg/man/plot.mresid.Rd |    2 +-
 7 files changed, 14 insertions(+), 12 deletions(-)

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Package deldir updated to version 0.0-9 with previous version 0.0-8 dated 2009-04-04

Author: Rolf Turner
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set.

Diff between deldir versions 0.0-8 dated 2009-04-04 and 0.0-9 dated 2009-11-04

 ChangeLog             |only
 DESCRIPTION           |    8 ++++----
 INDEX                 |    1 +
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 7 files changed, 11 insertions(+), 5 deletions(-)

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Package cem updated to version 1.0.127 with previous version 1.0.120 dated 2009-10-21

Author: Stefano Iacus Gary King Giuseppe Porro
Title: CEM: Software for Coarsened Exact Matching
Description: This program implements the coarsened exact matching algorithm (and many extensions) described in Stefano M. Iacus, Gary King, and Giuseppe Porro, "Causal Inference Without Balance Checking: Coarsened Exact Matching," http://gking.harvard.edu/files/abs/cem-plus-abs.shtml

Diff between cem versions 1.0.120 dated 2009-10-21 and 1.0.127 dated 2009-11-04

 DESCRIPTION           |    8 
 R/L1profile.R         |  131 -
 R/cem.main.R          |    2 
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 inst/doc/Rplots.pdf   |   50 
 inst/doc/cem.Rnw      |    2 
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 inst/doc/coarsen1.pdf |   28 
 inst/doc/coarsen2.pdf |   28 
 inst/doc/copyRd.Rout  |    2 
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 man/L1.profile.Rd     |   42 
 13 files changed, 2306 insertions(+), 3886 deletions(-)

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New package MFDF with initial version 0.0-2
Package: MFDF
Version: 0.0-2
Date: 2009-10-31
Title: Modeling Functional Data in Finance
Author: Wei Dou
Maintainer: Wei Dou
Depends: R (>= 2.4.0),fda,zoo
Suggests: odesolve, R.matlab, quadprog, DierckxSpline, nlme
Description: The package contains functions designed to modeling or analyzing the functional data arising in financial research and practice, as well as some interesting data sets.
License: GPL (>= 2)
Packaged: Tue Nov 3 16:53:57 2009; wd72
Repository: CRAN
Date/Publication: 2009-11-04 07:53:13

More information about MFDF at CRAN
Permanent link

Tue, 03 Nov 2009

Package spsurvey updated to version 2.1 with previous version 2.0 dated 2008-06-20

Author: Tom Kincaid and Tony Olsen with contributions from Don Stevens, Christian Platt, Denis White, and Richard Remington
Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms required for design and analysis of probability surveys such as those utilized by the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP).

Diff between spsurvey versions 2.0 dated 2008-06-20 and 2.1 dated 2009-11-03

 spsurvey-2.0/spsurvey/inst/doc/00Index.html    |only
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 spsurvey-2.1/spsurvey/R/albersgeod.r           |   79 +++++-----
 spsurvey-2.1/spsurvey/R/cat.analysis.s         |    5 
 spsurvey-2.1/spsurvey/R/category.est.s         |    3 
 spsurvey-2.1/spsurvey/R/cdf.test.s             |    8 -
 spsurvey-2.1/spsurvey/R/cont.analysis.s        |    5 
 spsurvey-2.1/spsurvey/R/cont.cdfplot.s         |    7 
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Package ff updated to version 2.1-0 with previous version 2.0.1 dated 2009-04-16

Author: Daniel Adler , Christian Gl\xE4ser , Oleg Nenadic , Jens Oehlschl\xE4gel , Walter Zucchini
Title: memory-efficient storage of large data on disk and fast access functions
Description: The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Diff between ff versions 2.0.1 dated 2009-04-16 and 2.1-0 dated 2009-11-03

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More information about ff at CRAN
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Package aroma.core updated to version 1.3.1 with previous version 1.2.0 dated 2009-09-10

Author: Henrik Bengtsson
Title: Support package for aroma.affymetrix et al.
Description: This package is a private support package for aroma.affymetrix et al. The methods and classes of this package are independent of platform. Its API is in alpha and beta stage.

Diff between aroma.core versions 1.2.0 dated 2009-09-10 and 1.3.1 dated 2009-11-03

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More information about aroma.core at CRAN
Permanent link

Package DoE.base updated to version 0.9-5 with previous version 0.9-4 dated 2009-09-25

Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.

Diff between DoE.base versions 0.9-4 dated 2009-09-25 and 0.9-5 dated 2009-11-03

 DESCRIPTION           |    8 ++++----
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Permanent link

Package rpartOrdinal updated to version 1.1 with previous version 1.0 dated 2009-07-18

Author: Kellie J. Archer
Title: Ordinal classification tree functions
Description: This package contains functions that can be called in conjunction with rpart for deriving a classification tree when the response to be predicted is ordinal.

Diff between rpartOrdinal versions 1.0 dated 2009-07-18 and 1.1 dated 2009-11-03

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More information about rpartOrdinal at CRAN
Permanent link

Package rSymPy updated to version 0.1-4 with previous version 0.1-2 dated 2009-01-11

Author: G Grothendieck
Title: R interface to SymPy computer algebra system
Description: Access SymPy computer algebra system from R via Jython

Diff between rSymPy versions 0.1-2 dated 2009-01-11 and 0.1-4 dated 2009-11-03

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Permanent link

Package MEMSS updated to version 0.3-6 with previous version 0.3-5 dated 2009-02-11

Author: Douglas Bates
Title: Data sets from Mixed-effects Models in S
Description: Data sets and sample analyses from Pinheiro and Bates, "Mixed-effects Models in S and S-PLUS" (Springer, 2000).

Diff between MEMSS versions 0.3-5 dated 2009-02-11 and 0.3-6 dated 2009-11-03

 DESCRIPTION |   16 ++++++++++------
 man/CO2.Rd  |   13 ++++++++-----
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More information about MEMSS at CRAN
Permanent link

Package distrDoc updated to version 2.2 with previous version 2.1.1 dated 2009-07-03

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Documentation for packages distr, distrEx, distrSim, distrTEst
Description: provides documentation in form of a common vignette to packages distr, distrEx, distrMod, distrSim, distrTEst

Diff between distrDoc versions 2.1.1 dated 2009-07-03 and 2.2 dated 2009-11-03

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 9 files changed, 16963 insertions(+), 16746 deletions(-)

More information about distrDoc at CRAN
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Package RandVar updated to version 0.7 with previous version 0.6.9 dated 2009-07-31

Author: Matthias Kohl, Peter Ruckdeschel
Title: Implementation of random variables
Description: Implementation of random variables by means of S4 classes and methods

Diff between RandVar versions 0.6.9 dated 2009-07-31 and 0.7 dated 2009-11-03

 DESCRIPTION                   |   15 +++---
 R/Expectation.R               |  102 +++++++++++++++++++++---------------------
 R/Matrixmult.R                |   12 ++--
 inst/NEWS                     |   56 +++++++++++++++++++++++
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 man/EuclRandVarList-class.Rd  |    6 +-
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Package xts updated to version 0.6-9 with previous version 0.6-8 dated 2009-10-14

Author: Jeffrey A. Ryan, Josh M. Ulrich
Title: Extensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.

Diff between xts versions 0.6-8 dated 2009-10-14 and 0.6-9 dated 2009-11-03

 DESCRIPTION         |    8 
 NAMESPACE           |    4 
 R/parse8601.R       |    4 
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Package sos updated to version 1.1-7 with previous version 1.1-5 dated 2009-10-01

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

Diff between sos versions 1.1-5 dated 2009-10-01 and 1.1-7 dated 2009-11-03

 DESCRIPTION      |    8 ++++----
 R/grepFn.R       |    4 ++--
 inst/doc/sos.pdf |    6 +++---
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 4 files changed, 11 insertions(+), 11 deletions(-)

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Package startupmsg updated to version 0.7 with previous version 0.6 dated 2009-04-15

Author: Peter Ruckdeschel
Title: Utilities for start-up messages
Description: Utilities for start-up messages

Diff between startupmsg versions 0.6 dated 2009-04-15 and 0.7 dated 2009-11-03

 DESCRIPTION             |   15 ++++++++-------
 NAMESPACE               |    2 +-
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New package omd with initial version 1.0
Package: omd
Type: Package
Title: filter the molecular descriptors for QSAR
Version: 1.0
Date: 2009-09-16
Author: Bin Ma
Maintainer: Bin Ma
Description: This package including two useful function, which can be used for filter the molecular descriptors matrix for QSAR.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-11-02 12:07:17 UTC; binma
Repository: CRAN
Date/Publication: 2009-11-03 11:27:28

More information about omd at CRAN
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New package optparse with initial version 0.8
Package: optparse
Type: Package
Title: Command line option parser.
Version: 0.8
Date: 2009-07-27
Author: Trevor Davis. "getopt" function, some documentation and unit tests ported from Allen Day's ``getopt`` package. Based on the optparse Python library by the Python Software Foundation.
Maintainer: Trevor Davis
Description: A command line parser inspired by Python's ``optparse`` libary to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
License: GPL (>= 2)
URL: http://r-forge.r-project.org/projects/optparse
LazyLoad: yes
Depends: R (>= 2.9.0), methods
Packaged: 2009-11-03 04:05:17 UTC; trevorld
Repository: CRAN
Date/Publication: 2009-11-03 11:27:30

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Package gstat updated to version 0.9-64 with previous version 0.9-63 dated 2009-10-05

Author: Edzer J. Pebesma and others
Title: 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.

Diff between gstat versions 0.9-63 dated 2009-10-05 and 0.9-64 dated 2009-11-03

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 R/fit.lmc.R            |    2 
 R/fit.variogram.reml.R |    3 
 R/gstat.R              |    5 
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 R/krige.cv.R           |    8 
 R/predict.gstat.R      |    3 
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Package gmvalid updated to version 1.21 with previous version 1.2 dated 2008-12-21

Author: Ronja Foraita, Fabian Sobotka
Title: Validation of graphical models
Description: Simulate data sets given a dependence model, validate graphical models using the bootstrap, find the best prediction model using cross validation.

Diff between gmvalid versions 1.2 dated 2008-12-21 and 1.21 dated 2009-11-03

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Package fds updated to version 1.2 with previous version 1.1 dated 2009-10-08

Author: Han Lin Shang and Rob J Hyndman
Title: Functional data sets
Description: Functional data sets

Diff between fds versions 1.1 dated 2009-10-08 and 1.2 dated 2009-11-03

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Package fExoticOptions updated to version 2110.77 with previous version 2100.76 dated 2009-09-29

Author: Diethelm Wuertz and many others, see the SOURCE file
Title: Exotic Option Valuation
Description: Environment for teaching "Financial Engineering and Computational Finance"

Diff between fExoticOptions versions 2100.76 dated 2009-09-29 and 2110.77 dated 2009-11-03

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 DESCRIPTION                   |   10 
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 R/BinaryOptions.R             |   76 +--
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 R/LookbackOptions.R           |  893 +++++++++++++++++++++---------------------
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Package epicalc updated to version 2.10.0.0 with previous version 2.9.2.8 dated 2009-10-16

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

Diff between epicalc versions 2.9.2.8 dated 2009-10-16 and 2.10.0.0 dated 2009-11-03

 DESCRIPTION              |    8 ++++----
 R/epicalc.R              |   27 +++++++++++++++++----------
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 3 files changed, 28 insertions(+), 20 deletions(-)

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Package distrTeach updated to version 2.2 with previous version 2.1 dated 2009-04-15

Author: Peter Ruckdeschel, Matthias Kohl, Anja Hueller, Eleonara Feist
Title: Extensions of package distr for teaching Stochastics/Statistics in secondary school
Description: Extensions of package distr and some additional functionality

Diff between distrTeach versions 2.1 dated 2009-04-15 and 2.2 dated 2009-11-03

 DESCRIPTION                |   17 +++++++++--------
 demo/illustCLT.R           |    1 +
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Package distrTEst updated to version 2.2 with previous version 2.1.1 dated 2009-07-31

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Estimation and Testing classes based on package distr
Description: Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way.

Diff between distrTEst versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03

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Package distrSim updated to version 2.2 with previous version 2.1.1 dated 2009-07-31

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Simulation classes based on package distr
Description: Simulation (S4-)classes based on package distr

Diff between distrSim versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03

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More information about distrSim at CRAN
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Package distrMod updated to version 2.2 with previous version 2.1.1 dated 2009-07-31

Author: Matthias Kohl, Peter Ruckdeschel
Title: Object orientated implementation of probability models
Description: Object orientated implementation of probability models based on packages 'distr' and 'distrEx'

Diff between distrMod versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03

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 distrMod-2.2/distrMod/R/0distrModUtils.R                  |   43 ++-
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Package distrEx updated to version 2.2 with previous version 2.1 dated 2009-04-15

Author: Matthias Kohl, Peter Ruckdeschel
Title: Extensions of package distr
Description: Extensions of package distr and some additional functionality

Diff between distrEx versions 2.1 dated 2009-04-15 and 2.2 dated 2009-11-03

 DESCRIPTION                             |   17 +-
 NAMESPACE                               |    5 
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 man/GPareto.Rd                          |only
 man/GParetoParameter-class.Rd           |only
 man/Gumbel-class.Rd                     |   32 ++--
 man/GumbelParameter-class.Rd            |    6 
 man/LMParameter-class.Rd                |    8 -
 man/MultivariateDistribution-class.Rd   |   24 ++-
 man/Pareto-class.Rd                     |   36 +++-
 man/Pareto.Rd                           |    2 
 man/ParetoParameter-class.Rd            |    6 
 man/PrognCondition-class.Rd             |    4 
 man/UnivariateCondDistribution-class.Rd |   26 ++-
 man/Var.Rd                              |   30 +++
 man/distrExConstants.Rd                 |    4 
 man/distrExOptions.Rd                   |    2 
 tests                                   |only
 40 files changed, 915 insertions(+), 189 deletions(-)

More information about distrEx at CRAN
Permanent link

New package distrEllipse with initial version 2.2
Package: distrEllipse
Version: 2.2
Date: 2009-10-16
Title: S4 classes for elliptically contoured distributions
Depends: R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2), distrEx(>= 2.2), distrSim(>= 2.2), startupmsg
Suggests: distrMod(>= 2.2), distrTEst(>= 2.2)
Author: Peter Ruckdeschel
Description: Distribution (S4-)classes for elliptically contoured distributions (based on package distr)
Maintainer: Peter Ruckdeschel
LazyLoad: yes
License: LGPL-3
URL: http://distr.r-forge.r-project.org/
Encoding: latin1
LastChangedDate: {$LastChangedDate: 2009-03-31 15:31:30 +0200 (Di, 31 Mrz 2009) $}
LastChangedRevision: {$LastChangedRevision: 447 $}
Packaged: 2009-11-03 09:41:47 UTC; btms02
Repository: CRAN
Date/Publication: 2009-11-03 13:49:22

More information about distrEllipse at CRAN
Permanent link

Package distr updated to version 2.2 with previous version 2.1.3 dated 2009-07-03

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Object orientated implementation of distributions
Description: Object orientated implementation of distributions

Diff between distr versions 2.1.3 dated 2009-07-03 and 2.2 dated 2009-11-03

 distr-2.1.3/distr/inst/doc/Rplots.pdf                 |only
 distr-2.1.3/distr/man/ContDistribution-class.Rd       |only
 distr-2.1.3/distr/man/ContDistribution.Rd             |only
 distr-2.2/distr/DESCRIPTION                           |   16 +
 distr-2.2/distr/NAMESPACE                             |   13 +
 distr-2.2/distr/R/0distrOptions.R                     |    5 
 distr-2.2/distr/R/AllClasses.R                        |  135 ++++++++++++++-
 distr-2.2/distr/R/AllGenerics.R                       |   27 ++-
 distr-2.2/distr/R/AllInitialize.R                     |   34 ++-
 distr-2.2/distr/R/CompoundDistribution.R              |   17 +
 distr-2.2/distr/R/ContDistribution.R                  |  158 ++++++++++++++----
 distr-2.2/distr/R/Convpow.r                           |   15 +
 distr-2.2/distr/R/DiscreteDistribution.R              |  154 ++++++++++++++---
 distr-2.2/distr/R/DistrList.R                         |   31 +++
 distr-2.2/distr/R/DistrSymmList.R                     |only
 distr-2.2/distr/R/Distribution.R                      |   12 +
 distr-2.2/distr/R/ExtraConvolutionMethods.R           |    5 
 distr-2.2/distr/R/Huberize.R                          |    8 
 distr-2.2/distr/R/LaplaceDistribution.R               |    6 
 distr-2.2/distr/R/LatticeDistribution.R               |   65 +++++--
 distr-2.2/distr/R/NormalDistribution.R                |   17 +
 distr-2.2/distr/R/PosDefSymmMatrix.R                  |only
 distr-2.2/distr/R/Symmetry.R                          |only
 distr-2.2/distr/R/Truncate.R                          |   25 ++
 distr-2.2/distr/R/UnivarLebDecDistribution.R          |   11 +
 distr-2.2/distr/R/UnivarMixingDistribution.R          |   54 ++++++
 distr-2.2/distr/R/bAcDcLcDistribution.R               |   29 ++-
 distr-2.2/distr/R/bAffLinUnivarLebDecDistribution.R   |   15 +
 distr-2.2/distr/R/internalUtils.R                     |    4 
 distr-2.2/distr/R/internalUtils_LCD.R                 |   17 +
 distr-2.2/distr/R/internalUtils_trunc.R               |    4 
 distr-2.2/distr/R/internals-qqplot.R                  |only
 distr-2.2/distr/R/print-show-methods.R                |    8 
 distr-2.2/distr/R/qqbounds.R                          |only
 distr-2.2/distr/R/qqplot.R                            |only
 distr-2.2/distr/R/setIsRelations.R                    |   15 -
 distr-2.2/distr/R/solve.R                             |only
 distr-2.2/distr/R/sqrt.R                              |only
 distr-2.2/distr/inst/MASKING                          |   29 ++-
 distr-2.2/distr/inst/NEWS                             |   62 +++++++
 distr-2.2/distr/inst/TOBEDONE                         |only
 distr-2.2/distr/inst/doc/newDistributions.Rnw         |   14 -
 distr-2.2/distr/inst/doc/newDistributions.pdf         |binary
 distr-2.2/distr/man/0distr-package.Rd                 |  134 ++++++++++-----
 distr-2.2/distr/man/AbscontDistribution-class.Rd      |only
 distr-2.2/distr/man/AbscontDistribution.Rd            |only
 distr-2.2/distr/man/Arcsine-class.Rd                  |   28 +--
 distr-2.2/distr/man/Beta-class.Rd                     |   30 ++-
 distr-2.2/distr/man/BetaParameter-class.Rd            |    8 
 distr-2.2/distr/man/Binom-class.Rd                    |   32 ++-
 distr-2.2/distr/man/BinomParameter-class.Rd           |    6 
 distr-2.2/distr/man/Cauchy-class.Rd                   |   30 ++-
 distr-2.2/distr/man/CauchyParameter-class.Rd          |    7 
 distr-2.2/distr/man/Chisq-class.Rd                    |   30 ++-
 distr-2.2/distr/man/ChisqParameter-class.Rd           |    6 
 distr-2.2/distr/man/CompoundDistribution-class.Rd     |   36 ++--
 distr-2.2/distr/man/DExp-class.Rd                     |   30 ++-
 distr-2.2/distr/man/Dirac-class.Rd                    |   34 ++-
 distr-2.2/distr/man/DiracParameter-class.Rd           |    4 
 distr-2.2/distr/man/DiscreteDistribution-class.Rd     |   56 +++---
 distr-2.2/distr/man/DiscreteDistribution.Rd           |   22 +-
 distr-2.2/distr/man/DistrList-class.Rd                |    2 
 distr-2.2/distr/man/DistrList.Rd                      |   11 -
 distr-2.2/distr/man/DistrSymmList-class.Rd            |only
 distr-2.2/distr/man/DistrSymmList.Rd                  |only
 distr-2.2/distr/man/Distribution-class.Rd             |   29 ++-
 distr-2.2/distr/man/DistributionSymmetry-class.Rd     |only
 distr-2.2/distr/man/EllipticalSymmetry-class.Rd       |only
 distr-2.2/distr/man/EllipticalSymmetry.Rd             |only
 distr-2.2/distr/man/EuclideanSpace-class.Rd           |    4 
 distr-2.2/distr/man/Exp-class.Rd                      |   24 ++
 distr-2.2/distr/man/ExpOrGammaOrChisq-class.Rd        |    3 
 distr-2.2/distr/man/ExpParameter-class.Rd             |    4 
 distr-2.2/distr/man/FParameter-class.Rd               |    9 -
 distr-2.2/distr/man/Fd-class.Rd                       |   32 ++-
 distr-2.2/distr/man/GammaParameter-class.Rd           |    6 
 distr-2.2/distr/man/Gammad-class.Rd                   |   31 ++-
 distr-2.2/distr/man/Geom-class.Rd                     |   32 ++-
 distr-2.2/distr/man/GeomParameter-class.Rd            |    4 
 distr-2.2/distr/man/Hyper-class.Rd                    |   34 ++-
 distr-2.2/distr/man/HyperParameter-class.Rd           |    8 
 distr-2.2/distr/man/Integer-class.Rd                  |    4 
 distr-2.2/distr/man/Lattice-class.Rd                  |    8 
 distr-2.2/distr/man/LatticeDistribution-class.Rd      |   40 ++--
 distr-2.2/distr/man/LatticeDistribution.Rd            |   25 +-
 distr-2.2/distr/man/Lnorm-class.Rd                    |   30 ++-
 distr-2.2/distr/man/LnormParameter-class.Rd           |    6 
 distr-2.2/distr/man/Logis-class.Rd                    |   30 ++-
 distr-2.2/distr/man/LogisParameter-class.Rd           |    6 
 distr-2.2/distr/man/Math-methods.Rd                   |    8 
 distr-2.2/distr/man/Naturals-class.Rd                 |    4 
 distr-2.2/distr/man/Nbinom-class.Rd                   |   32 ++-
 distr-2.2/distr/man/NbinomParameter-class.Rd          |    6 
 distr-2.2/distr/man/NoSymmetry-class.Rd               |only
 distr-2.2/distr/man/NoSymmetry.Rd                     |only
 distr-2.2/distr/man/Norm-class.Rd                     |   30 ++-
 distr-2.2/distr/man/NormParameter-class.Rd            |    6 
 distr-2.2/distr/man/Parameter-class.Rd                |    2 
 distr-2.2/distr/man/Pois-class.Rd                     |   32 ++-
 distr-2.2/distr/man/PoisParameter-class.Rd            |    4 
 distr-2.2/distr/man/PosDefSymmMatrix-class.Rd         |only
 distr-2.2/distr/man/PosDefSymmMatrix.Rd               |only
 distr-2.2/distr/man/Reals-class.Rd                    |    4 
 distr-2.2/distr/man/SphericalSymmetry-class.Rd        |only
 distr-2.2/distr/man/SphericalSymmetry.Rd              |only
 distr-2.2/distr/man/Symmetry-class.Rd                 |only
 distr-2.2/distr/man/TParameter-class.Rd               |    6 
 distr-2.2/distr/man/Td-class.Rd                       |   30 ++-
 distr-2.2/distr/man/UniNormParameter-class.Rd         |    6 
 distr-2.2/distr/man/Unif-class.Rd                     |   26 +-
 distr-2.2/distr/man/UnifParameter-class.Rd            |    6 
 distr-2.2/distr/man/UnivarDistrList-class.Rd          |    2 
 distr-2.2/distr/man/UnivarDistrList.Rd                |   10 -
 distr-2.2/distr/man/UnivarLebDecDistribution-class.Rd |   66 ++++---
 distr-2.2/distr/man/UnivarMixingDistribution-class.Rd |   45 +++--
 distr-2.2/distr/man/UnivarMixingDistribution.Rd       |    2 
 distr-2.2/distr/man/UnivariateDistribution-class.Rd   |   30 ++-
 distr-2.2/distr/man/Weibull-class.Rd                  |   30 ++-
 distr-2.2/distr/man/WeibullParameter-class.Rd         |    6 
 distr-2.2/distr/man/distroptions.Rd                   |   12 +
 distr-2.2/distr/man/internalClassUnions-class.Rd      |only
 distr-2.2/distr/man/internals-qqplot.Rd               |only
 distr-2.2/distr/man/internals.Rd                      |    2 
 distr-2.2/distr/man/operators-methods.Rd              |    2 
 distr-2.2/distr/man/options.Rd                        |    6 
 distr-2.2/distr/man/plot-methods.Rd                   |   20 +-
 distr-2.2/distr/man/qqbounds.Rd                       |only
 distr-2.2/distr/man/qqplot.Rd                         |only
 distr-2.2/distr/man/rSpace-class.Rd                   |    2 
 distr-2.2/distr/man/solve-methods.Rd                  |only
 distr-2.2/distr/man/sqrt-methods.Rd                   |only
 distr-2.2/distr/tests                                 |only
 132 files changed, 1630 insertions(+), 687 deletions(-)

More information about distr at CRAN
Permanent link

Package cobs99 updated to version 0.9-8 with previous version 0.9-7 dated 2007-10-09

Author: Pin T. Ng and Xuming He, U. Illinois; R port by Martin Maechler
Title: Constrained B-splines -- outdated 1999 version
Description: Qualitatively Constrained (Regression) Smoothing via Linear Programming. OUTDATED version based on He & Ng (1999), the modified "non-simplex" algorithm of Bartels and Conn (1980).

Diff between cobs99 versions 0.9-7 dated 2007-10-09 and 0.9-8 dated 2009-11-03

 ChangeLog                 |    8 ++++++++
 DESCRIPTION               |   22 ++++++++++++----------
 man/cobs.Rd               |    6 +++---
 man/cobsOld.Rd            |    7 +++----
 man/predict.cobs.Rd       |    3 ---
 man/qbsks.Rd              |    2 --
 tests/small-ex.Rout.save  |    4 ++--
 tests/spline-ex.Rout.save |   24 ++++++++++++------------
 8 files changed, 40 insertions(+), 36 deletions(-)

More information about cobs99 at CRAN
Permanent link

Package aroma.affymetrix updated to version 1.3.0 with previous version 1.2.0 dated 2009-09-10

Author: Henrik Bengtsson , Ken Simpson , Elizabeth Purdom , Mark Robinson
Title: Analysis of large Affymetrix microarray data sets
Description: This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the diskspace that limits what number of arrays can be analyzed.

Diff between aroma.affymetrix versions 1.2.0 dated 2009-09-10 and 1.3.0 dated 2009-11-03

 aroma.affymetrix-1.2.0/aroma.affymetrix/man/fromFiles.AffymetrixFileSet.Rd                                                               |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/DESCRIPTION                                                                                      |   26 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCdfFile.R                                                                            |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelFile.R                                                                            |    7 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.R                                                                             |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.extractSnpFeatureSet.R                                                        |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.importFromDChip.R                                                             |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.xtras.R                                                                       |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSetTuple.R                                                                        |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpFile.R                                                                          |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpSet.R                                                                           |   11 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R                                                                    |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCsvFile.R                                                                            |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixFileSet.R                                                                            |   12 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R                                                                       |    9 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixTsvFile.R                                                                            |    5 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaCellMatchScoreFile.R                                                                      |    5 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaCellSequenceFile.AFFX.R                                                                   |   56 +++
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUfcFile.R                                                                                 |    7 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUflFile.R                                                                                 |    5 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUnitGcContentFile.R                                                                       |    5 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChipEffectGroupMerge.R                                                                         |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChipEffectSet.R                                                                                |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.R                                                                              |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R                                                                |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R                                                              |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnPlm.R                                                                                        |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnagCfhFile.R                                                                                  |    7 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnagCfhSet.R                                                                                   |   24 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CrlmmModel.R                                                                                   |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CrlmmParametersSet.R                                                                           |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipCdfBinFile.R                                                                              |    1 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpFile.R                                                                                 |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpSet.R                                                                                  |   11 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpSet.extras.R                                                                           |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ExonChipEffectSet.R                                                                            |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ExonRmaPlm.R                                                                                   |   12 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/FirmaSet.R                                                                                     |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/PdInfo2Cdf.R                                                                                   |  162 ++++++----
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R                                                           |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/QualityAssessmentModel.R                                                                       |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ResidualSet.R                                                                                  |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/RmaPlm.R                                                                                       |  128 +++++--
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/SnpChipEffectSet.R                                                                             |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/SnpPlm.R                                                                                       |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/Transform.R                                                                                    |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/R/WeightsSet.R                                                                                   |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/incl/999.missingdocs.txt                                                                         |   18 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/CITATION                                                                                    |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/NEWS                                                                                        |   36 ++
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/extractAffyBatch.R                         |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240,Xba240/20091016,extractSnpFeatureSet.R |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20090901,6.0,CRMAv2,ASCN,TumorBoost.R      |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20090927,gcrmabg.R                          |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuGene-1_0-st-v1                                               |only
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd                                                                         |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCelFile.Rd                                                                         |   21 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCelSet.Rd                                                                          |   21 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd                                                                        |   22 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixFile.Rd                                                                            |   17 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixFileSet.Rd                                                                         |   18 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd                                                                    |   19 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd                                                               |   19 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChipEffectFile.Rd                                                                            |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChipEffectSet.Rd                                                                             |   25 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnChipEffectFile.Rd                                                                          |   31 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnChipEffectSet.Rd                                                                           |   33 +-
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnPlm.Rd                                                                                     |    8 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd                                                                       |   31 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnagCfhFile.Rd                                                                               |   17 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnagCfhSet.Rd                                                                                |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CrlmmParametersFile.Rd                                                                       |   21 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CrlmmParametersSet.Rd                                                                        |   19 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipCdfBinFile.Rd                                                                           |   23 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipDcpFile.Rd                                                                              |   17 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipDcpSet.Rd                                                                               |   22 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipGenomeInformation.Rd                                                                    |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipSnpInformation.Rd                                                                       |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonChipEffectFile.Rd                                                                        |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonChipEffectSet.Rd                                                                         |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd                                                                     |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonRmaPlm.Rd                                                                                |   14 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/FirmaFile.Rd                                                                                 |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/FirmaSet.Rd                                                                                  |   25 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/GenomeInformation.Rd                                                                         |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd                                                                            |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddPlm.Rd                                                                              |    6 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd                                                                           |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/Model.Rd                                                                                     |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd                                                                       |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/Non-documented_objects.Rd                                                                    |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ParameterCelFile.Rd                                                                          |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ParameterCelSet.Rd                                                                           |   23 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ProbeAffinityFile.Rd                                                                         |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ProbeLevelModel.Rd                                                                           |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/QualityAssessmentFile.Rd                                                                     |   25 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/QualityAssessmentSet.Rd                                                                      |   23 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ResidualFile.Rd                                                                              |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ResidualSet.Rd                                                                               |   23 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaCnPlm.Rd                                                                                  |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaPlm.Rd                                                                                    |    5 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaSnpPlm.Rd                                                                                 |    4 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpChipEffectFile.Rd                                                                         |   31 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpChipEffectSet.Rd                                                                          |   29 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpInformation.Rd                                                                            |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpPlm.Rd                                                                                    |   12 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd                                                                      |   31 +
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/UgpGenomeInformation.Rd                                                                      |   15 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/UnitModel.Rd                                                                                 |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/WeightsFile.Rd                                                                               |   27 -
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/WeightsSet.Rd                                                                                |   23 -
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 aroma.affymetrix-1.3.0/aroma.affymetrix/man/getResiduals.QualityAssessmentModel.Rd                                                       |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/importFromDChip.AffymetrixCelSet.Rd                                                          |    2 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/isDuplicated.AffymetrixCelSet.Rd                                                             |   14 
 aroma.affymetrix-1.3.0/aroma.affymetrix/man/isDuplicated.CnagCfhSet.Rd                                                                   |   14 
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Permanent link

Package analogue updated to version 0.6-21 with previous version 0.6-8 dated 2009-05-07

Author: Gavin L. Simpson, Jari Oksanen
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.

Diff between analogue versions 0.6-8 dated 2009-05-07 and 0.6-21 dated 2009-11-03

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Permanent link

Package ade4 updated to version 1.4-13 with previous version 1.4-11 dated 2009-04-04

Author: Daniel Chessel, Anne-Beatrice Dufour and Stephane Dray , with contributions from Thibaut Jombart, Jean R. Lobry, Sebastien Ollier, Sandrine Pavoine and Jean Thioulouse.
Title: Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences
Description: Multivariate data analysis and graphical display.

Diff between ade4 versions 1.4-11 dated 2009-04-04 and 1.4-13 dated 2009-11-03

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Package TraMineR updated to version 1.4-1 with previous version 1.4 dated 2009-08-06

Author: Alexis Gabadinho , Matthias Studer , Nicolas S. Muller , Gilbert Ritschard .
Title: Sequences and trajectories mining for social scientists
Description: This package is a toolbox for sequence manipulation, description, rendering and more generally sequence data mining in the field of social sciences. Though it is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers its features apply indeed also to many other kinds of categorical sequence data. It accepts as input many different sequence representations and provides tools for translating sequences from one format to another. It offers several statistical functions for describing and rendering sequences, for computing distances between sequences with different metrics among which optimal matching, the longest common prefix and the longest common subsequence, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on TraMineR's web page.

Diff between TraMineR versions 1.4 dated 2009-08-06 and 1.4-1 dated 2009-11-03

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Permanent link

Package TWIX updated to version 0.2.10 with previous version 0.2.6 dated 2008-11-28

Author: Sergej Potapov
Title: Trees WIth eXtra splits
Description: Trees with extra splits

Diff between TWIX versions 0.2.6 dated 2008-11-28 and 0.2.10 dated 2009-11-03

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Package SweaveListingUtils updated to version 0.4 with previous version 0.3.3 dated 2009-07-31

Author: Peter Ruckdeschel
Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most recent version (or another url) thereby avoiding inconsistencies between vignette and documented source code

Diff between SweaveListingUtils versions 0.3.3 dated 2009-07-31 and 0.4 dated 2009-11-03

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Package RcppTemplate updated to version 6.0 with previous version 5.2 dated 2006-11-28

Author: Dominick Samperi
Title: Demo Package for Rcpp R/C++ Object Mapping and Library
Description: The Rcpp class library enables C++ to speak the language of R. The library maps the most commonly used R data structures to C++ classes. This includes vectors, matrices, factors, dates, data frames, time series, and functions. R can call C++ functions, and C++ objects can call R functions, and the parameters and return values can be of any of the types just mentioned. This package serves two roles: 1. it serves as a demo package for Rcpp, and 2. it serves as a template for the creation of new packages that use the Rcpp library (and also for packages that do not). An important goal of the library is to support the creation of high-performance packages that do heavy computations on large data sets where a hybrid R/C++ strategy is the best fit. See the document RcppDoc.pdf for more information.

Diff between RcppTemplate versions 5.2 dated 2006-11-28 and 6.0 dated 2009-11-03

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Package R.filesets updated to version 0.6.5 with previous version 0.5.3 dated 2009-08-14

Author: Henrik Bengtsson
Title: Easy handling of and access to files organized in structured directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterative suchs sets. The API is designed such that these classes can be subsetted to provide for instance a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have fullnames which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.

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Package FAiR updated to version 0.4-5 with previous version 0.4-4 dated 2009-01-12

Author: Ben Goodrich
Title: Factor Analysis in R
Description: This package estimates factor analysis models using a genetic algorithm, which permits a general mechanism for restricted optimization with arbitrary restrictions that are chosen at run time with the help of a GUI. Importantly, inequality restrictions can be imposed on functions of multiple parameters, which provides a new avenues for testing and generating theories with factor analysis models. This package also includes an entirely new estimator of the common factor analysis model called semi-exploratory factor analysis, which is a general alternative to exploratory and confirmatory factor analysis. Finally, this package integrates a lot of other packages that estimate sample covariance matrices and thus provides a lot of alternatives to the traditional sample covariance calculation. Note that you need to have the Gtk run time library installed on your system to use this package; see the URL below for detailed installation instructions. Most users would only need to understand the first twenty-four pages of the PDF manual.

Diff between FAiR versions 0.4-4 dated 2009-01-12 and 0.4-5 dated 2009-11-03

 DESCRIPTION             |   35 +
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New package MaXact with initial version 0.1
Package: MaXact
Type: Package
Title: Exact max-type Cochran-Armitage trend test(CATT)
Version: 0.1
Date: 2009-10-31
Author: Jianan Tian , Chenliang Xu
Maintainer: Chenliang Xu
Depends: R (>= 2.2.0), mnormt
Description: Perform exact MAX3 or MAX2 test for one-locus genetic association analysis and trend test for dominant, recessive and additive models. It can also calculate approximated p-value with the normal approximation method.
License: GPL-2
Packaged: Mon Nov 2 16:24:30 2009; lucky
Repository: CRAN
Date/Publication: 2009-11-03 11:23:42

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Package mapproj updated to version 1.1-8.2 with previous version 1.1-7.2 dated 2008-08-06

Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P Minka, transition to Plan 9 codebase by Roger Bivand.
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.

Diff between mapproj versions 1.1-7.2 dated 2008-08-06 and 1.1-8.2 dated 2009-11-03

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Mon, 02 Nov 2009

Package tframePlus updated to version 2009.10-2 with previous version 2009.10-1 dated 2009-10-18

Author: Paul Gilbert
Title: Time Frame coding kernel extensions
Description: Extensions and additional tframe utilities.

Diff between tframePlus versions 2009.10-1 dated 2009-10-18 and 2009.10-2 dated 2009-11-02

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Package prob updated to version 0.9-2 with previous version 0.9-1 dated 2008-01-09

Author: G. Jay Kerns
Title: Elementary Probability on Finite Sample Spaces
Description: This package provides a framework for performing elementary probability calculations on finite sample spaces, which may be represented by data frames or lists. Functionality includes setting up sample spaces, counting tools, defining probability spaces, performing set algebra, calculating probability and conditional probability, tools for simulation and checking the law of large numbers, adding random variables, and finding marginal distributions. Characteristic functions for all base R distributions are included.

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Package animation updated to version 1.0-7 with previous version 1.0-6 dated 2009-10-26

Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of 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.

Diff between animation versions 1.0-6 dated 2009-10-26 and 1.0-7 dated 2009-11-02

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Package R.utils updated to version 1.2.4 with previous version 1.2.2 dated 2009-10-18

Author: Henrik Bengtsson
Title: Various programming utilities
Description: This package provides utility classes and methods useful when programming in R and developing R packages.

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Package R.oo updated to version 1.6.5 with previous version 1.6.2 dated 2009-10-19

Author: Henrik Bengtsson
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.

Diff between R.oo versions 1.6.2 dated 2009-10-19 and 1.6.5 dated 2009-11-02

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Package R.matlab updated to version 1.2.6 with previous version 1.2.5 dated 2009-09-03

Author: Henrik Bengtsson , Jason Riedy
Title: Read and write of MAT files together with R-to-Matlab connectivity
Description: This package provides methods to read and write MAT files. It also makes it possible to communicate (evaluate code, send and retrieve objects etc.) with Matlab v6 or higher running locally or on a remote host.

Diff between R.matlab versions 1.2.5 dated 2009-09-03 and 1.2.6 dated 2009-11-02

 DESCRIPTION             |   10 ++---
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Package MTSKNN updated to version 0.0-2 with previous version 0.0-1 dated 2009-10-27

Author: Peng Dai and Wei Dou
Title: Multivariate two-sample tests based on K-nearest-neighbors
Description: The package contains three multivariate two-sample tests which are all based on k-nearest-neighbors. The testing procedures are distribution free and are robust from balanced designs to unbalanced designs.

Diff between MTSKNN versions 0.0-1 dated 2009-10-27 and 0.0-2 dated 2009-11-02

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New package MCMCtNARCH with initial version 1.0
Package: MCMCtNARCH
Version: 1.0
Date: 2009-10-31
Title: MCMCtNARCH package
Author: Ken Ren
Maintainer: Ken Ren
Depends: R (>= 2.0.1)
Description: MCMC estimation for Box-Cox transformed GARCH (1, 1) with Student-t distribution using the random-walk MetropolisHastings algorithm.
License: GPL (>= 2)
Packaged: Mon Nov 2 18:21:32 2009; @work
Repository: CRAN
Date/Publication: 2009-11-02 07:46:19

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New package MCMCtGARCH with initial version 1.0
Package: MCMCtGARCH
Version: 1.0
Date: 2009-10-31
Title: MCMCtGARCH package
Author: Ken Ren
Maintainer: Ken Ren
Depends: R (>= 2.0.1)
Description: MCMC estimation for GARCH (1, 1) with Student-t distribution using the random-walk MetropolisHastings algorithm.
License: GPL (>= 2)
Packaged: Mon Nov 2 17:11:50 2009; @work
Repository: CRAN
Date/Publication: 2009-11-02 07:46:18

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New package MCMCtGARCHM with initial version 1.0
Package: MCMCtGARCHM
Version: 1.0
Date: 2009-10-31
Title: MCMCtGARCHM package
Author: Ken Ren
Maintainer: Ken Ren
Depends: R (>= 2.0.1)
Description: MCMC estimation for GARCH (1, 1) in mean with Student-t distribution using the random-walk MetropolisHastings algorithm.
License: GPL (>= 2)
Packaged: Mon Nov 2 18:14:56 2009; @work
Repository: CRAN
Date/Publication: 2009-11-02 07:46:16

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Package Deducer updated to version 0.2-0 with previous version 0.1-0 dated 2009-08-02

Author: Ian Fellows
Title: Deducer
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Some integration with the Windows Rgui has been done.

Diff between Deducer versions 0.1-0 dated 2009-08-02 and 0.2-0 dated 2009-11-02

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Sun, 01 Nov 2009

Package runjags updated to version 0.9.5-2 with previous version 0.9.5-1 dated 2009-10-15

Author: Matthew Denwood (funded as part of the DEFRA VTRI project 0101).
Title: Run Bayesian MCMC Models in the BUGS syntax from Within R
Description: A set of functions to allow any user specified model to be run in JAGS from within R, returning the MCMC chains as R objects. Includes functions to read external WinBUGS type textfiles, and allows several ways of automatically specifying model data from existing R objects or R functions. Also includes functions to automatically calculate model run length, autocorrealtion and Gelman Rubin statistic diagnostics for all models to simplify the process of achieving chain convergence. Designed for maximum compatibility with WinBUGS syntax, although minor modification to existing .bug files will be required. Requires Just Another Gibbs Sampler (JAGS) for most functions, see: http://www-fis.iarc.fr/~martyn/software/jags/

Diff between runjags versions 0.9.5-1 dated 2009-10-15 and 0.9.5-2 dated 2009-11-01

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 2 files changed, 6 insertions(+), 6 deletions(-)

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Package rjson updated to version 0.1.8 with previous version 0.1.7 dated 2009-08-28

Author: Alex Couture-Beil
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa

Diff between rjson versions 0.1.7 dated 2009-08-28 and 0.1.8 dated 2009-11-01

 DESCRIPTION                  |    6 +++---
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Package quantmod updated to version 0.3-13 with previous version 0.3-12 dated 2009-10-03

Author: Jeffrey A. Ryan
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies

Diff between quantmod versions 0.3-12 dated 2009-10-03 and 0.3-13 dated 2009-11-01

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Package fingerprint updated to version 3.2 with previous version 3.1.2 dated 2009-02-23

Author: Rajarshi Guha
Title: Functions to operate on binary fingerprint data
Description: This package contains functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint' which is internally represented a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.

Diff between fingerprint versions 3.1.2 dated 2009-02-23 and 3.2 dated 2009-11-01

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New package phylobase with initial version 0.5
Package: phylobase
Type: Package
Title: Base package for phylogenetic structures and comparative data
Version: 0.5
Date: 2009-10-30
Depends: methods, grid, ape(>= 2.1)
Suggests: ade4, MASS
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Ben Bolker
Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
License: GPL (>= 2)
Collate: phylo4.R checkdata.R formatData.R class-multiphylo4.R class-oldclasses.R class-phylo4.R class-phylo4d.R class-phylomats.R methods-multiphylo4.R methods-oldclasses.R methods-phylo4.R methods-phylo4d.R setAs-Methods.R pdata.R subset.R prune.R treePlot.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R
URL: http://phylobase.R-forge.R-project.org
Repository: CRAN
Repository/R-Forge/Project: phylobase
Repository/R-Forge/Revision: 700
Date/Publication: 2009-11-01 18:04:14
Packaged: 2009-10-31 21:15:49 UTC; rforge

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New package equate with initial version 0.1-0
Package: equate
Version: 0.1-0
Date: 2009-10-30
Title: Traditional Methods for Test Score Equating
Author: Anthony Albano
Maintainer: Anthony Albano
Depends: R (>= 2.8.0)
Description: In educational and psychological measurement multiple forms of a test are often created, where forms are intended to be identical in difficulty and statistical characteristics. In the likely case that forms differ in difficulty, statistical methods of equating and linking allow for the conversion of scores on one form to the scale of another, essentially creating parallel forms. The equate package contains functions for traditional equating, including mean, linear, and equipercentile equating and methods for pre- and post-smoothing of score distributions.
License: GPL (>= 2)
URL: http://www.r-project.org, albanofile.com
Packaged: 2009-10-31 19:23:34 UTC; hp
Repository: CRAN
Date/Publication: 2009-11-01 17:33:43

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Package bestglm updated to version 0.20 with previous version 0.14 dated 2009-10-19

Author: A.I. McLeod and Changjiang Xu
Title: Best Subset GLM
Description: Best subset glm using AIC, BIC, EBIC, BICq or Cross-Validation. For the normal case, the 'leaps' is used. Otherwise, a slower exhaustive search. The 'xtable' package is needed for vignette 'SimExperimentBICq.Rnw' accompanying this package.

Diff between bestglm versions 0.14 dated 2009-10-19 and 0.20 dated 2009-11-01

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Package SoPhy updated to version 1.0.39 with previous version 1.0.36 dated 2009-01-14

Author: R by Martin Schlather ; FORTRAN by Rien van Genuchten, Carl A. Mendoza, Rene Therrien, Edward Sudicky
Title: Soil Physics Tools
Description: SWMS_2D interface

Diff between SoPhy versions 1.0.36 dated 2009-01-14 and 1.0.39 dated 2009-11-01

 DESCRIPTION          |   16 +++++++++++-----
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Package RcmdrPlugin.qual updated to version 0.3.0 with previous version 0.1.0 dated 2009-08-21

Author: Erin Hodgess
Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the Quality control class Stat 4300

Diff between RcmdrPlugin.qual versions 0.1.0 dated 2009-08-21 and 0.3.0 dated 2009-11-01

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Package RandomFields updated to version 1.3.41 with previous version 1.3.40 dated 2009-07-01

Author: Martin Schlather
Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging

Diff between RandomFields versions 1.3.40 dated 2009-07-01 and 1.3.41 dated 2009-11-01

 DESCRIPTION         |    6 +++---
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Package MarkedPointProcess updated to version 0.2.13 with previous version 0.2.11 dated 2009-06-29

Author: Martin Schlather
Title: Analysis of Marks of Marked Point Processes
Description: Non-parametric Analysis of the Marks of Marked Point Processes

Diff between MarkedPointProcess versions 0.2.11 dated 2009-06-29 and 0.2.13 dated 2009-11-01

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Package GLDEX updated to version 1.0.3.3 with previous version 1.0.3.2 dated 2009-10-11

Author: Steve Su
Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Discretised and Maximum Likelihood Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood estimation. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.

Diff between GLDEX versions 1.0.3.2 dated 2009-10-11 and 1.0.3.3 dated 2009-11-01

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Package DierckxSpline updated to version 1.1-4 with previous version 1.1-3 dated 2009-04-16

Author: Sundar Dorai-Raj and Spencer Graves
Title: R companion to "Curve and Surface Fitting with Splines"
Description: This package provides a wrapper to the FITPACK routines written by Paul Dierckx. The original Fortran is available from http://www.netlib.org/dierckx

Diff between DierckxSpline versions 1.1-3 dated 2009-04-16 and 1.1-4 dated 2009-11-01

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New package stockPortfolio with initial version 1.0
Package: stockPortfolio
Type: Package
Title: Build stock models and analyze stock portfolios.
Version: 1.0
Date: 2009-10-21
Author: David Diez and Nicolas Christou
Maintainer: David Diez
Description: Download stock data, build single index, constant correlation, and multigroup models, and estimate optimal stock portfolios. Plotting functions for the portfolio possibilities curve and portfolio cloud are included. A function to test a portfolio on a data set is also provided.
License: GPL-2
LazyLoad: yes
Packaged: Thu Oct 29 14:59:48 2009; diez
Repository: CRAN
Date/Publication: 2009-11-01 16:17:46

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Package scrime updated to version 1.1.9 with previous version 1.1.7 dated 2009-10-14

Author: Holger Schwender, Arno Fritsch
Title: Analysis of High-Dimensional Categorical Data such as SNP Data
Description: Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.

Diff between scrime versions 1.1.7 dated 2009-10-14 and 1.1.9 dated 2009-11-01

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Package rcdklibs updated to version 1.2.3 with previous version 1.2.2 dated 2009-10-29

Author: Rajarshi Guha
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

Diff between rcdklibs versions 1.2.2 dated 2009-10-29 and 1.2.3 dated 2009-11-01

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Package rcdk updated to version 2.9.6 with previous version 2.9.4 dated 2009-08-24

Author: Rajarshi Guha
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.

Diff between rcdk versions 2.9.4 dated 2009-08-24 and 2.9.6 dated 2009-11-01

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Package rJava updated to version 0.8-1 with previous version 0.8-0 dated 2009-10-28

Author: Simon Urbanek
Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.

Diff between rJava versions 0.8-0 dated 2009-10-28 and 0.8-1 dated 2009-11-01

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Package nodeHarvest updated to version 0.2 with previous version 0.1 dated 2009-10-12

Author: Nicolai Meinshausen
Title: Node Harvest for regression and classification
Description: Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction.

Diff between nodeHarvest versions 0.1 dated 2009-10-12 and 0.2 dated 2009-11-01

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Package gWidgetsWWW updated to version 0.0-12 with previous version 0.0-11 dated 2009-08-23

Author: John Verzani
Title: Toolkit implementation of the gWidgets API for use with web pages
Description: Port of the gWidgets API to www using a local server or RApache (http://biostat.mc.vanderbilt.edu/rapache/index.html) to link R with a web page, The Ext JavaScript libararies are used to create and manipulate widgets. (www.extjs.com)

Diff between gWidgetsWWW versions 0.0-11 dated 2009-08-23 and 0.0-12 dated 2009-11-01

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