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

 DESCRIPTION           |   14 ++---
 R/clean.R             |   17 +++---
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 10 files changed, 196 insertions(+), 75 deletions(-)

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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

 DESCRIPTION               |    8 ++++----
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 data/dataset.rda          |binary
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 man/modTempEff-package.Rd |    4 ++--
 9 files changed, 59 insertions(+), 19 deletions(-)

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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 +++---
 src/fcn_lmder.c |    7 +------
 src/fcn_lmdif.c |    7 +------
 src/nls_lm.c    |    4 ++--
 4 files changed, 7 insertions(+), 17 deletions(-)

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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

 DESCRIPTION              |    8 -
 NAMESPACE                |    3 
 R/REXP_joint.R           |    6 
 R/cgFbatCode.R           |   83 +++++++++-
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 30 files changed, 952 insertions(+), 171 deletions(-)

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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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 ecolMod-1.2.2/ecolMod/DESCRIPTION       |   40 ++++++++++++++++++++------------
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 5 files changed, 31 insertions(+), 18 deletions(-)

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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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 deSolve-1.5-1/deSolve/NAMESPACE                  |    7 
 deSolve-1.5-1/deSolve/R/Utilities.R              |    2 
 deSolve-1.5-1/deSolve/R/diagnostics.R            |    9 
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 17 files changed, 585 insertions(+), 579 deletions(-)

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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

 DESCRIPTION                  |   10 
 R/autoKrige.r                |    6 
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 SvnLog                       |   39 +++
 man/autoKrige.rd             |    7 
 man/autoKrige_cv.rd          |    6 
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 tests/automap.R              |    5 
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 11 files changed, 119 insertions(+), 505 deletions(-)

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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

 ChangeLog                 |   43 ++++++++++++++++++++++++++++++++++++++++++-
 DESCRIPTION               |    8 ++++----
 R/ace.R                   |    3 ++-
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 46 files changed, 215 insertions(+), 145 deletions(-)

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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.

Diff between AlgDesign versions 1.0-12 dated 2009-09-30 and 1.1-0 dated 2009-11-23

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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

 DESCRIPTION   |    8 ++++----
 R/AAoptions.S |   16 ++++++++--------
 R/emu.track.S |   38 ++++++++++++++++++++++++++++++--------
 3 files changed, 42 insertions(+), 20 deletions(-)

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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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 6 files changed, 37 insertions(+), 32 deletions(-)

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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.

Diff between oosp versions 0.2.2 dated 2009-11-22 and 0.2.3 dated 2009-11-23

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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

 DESCRIPTION                      |    8 
 NAMESPACE                        |    1 
 R/glmmPQL.R                      |    3 
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 R/rlm.R                          |   29 +--
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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

 DESCRIPTION  |   10 
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 3 files changed, 671 insertions(+), 155 deletions(-)

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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

 CHANGELOG       |    4 ++++
 DESCRIPTION     |    8 +++-----
 NAMESPACE       |    1 +
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