Tue, 21 Jul 2009

Package mboost updated to version 1.1-2 with previous version 1.1-1 dated 2009-04-22

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.

Diff between mboost versions 1.1-1 dated 2009-04-22 and 1.1-2 dated 2009-07-21

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Package iterators updated to version 1.0.2 with previous version 1.0.1 dated 2009-06-30

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

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Package bnlearn updated to version 1.5 with previous version 1.4.1 dated 2009-06-14

Author: Marco Scutari
Title: Bayesian network structure learning
Description: Bayesian network structure learning via constraint-based (also known as 'conditional independence') and score-based algorithms. This package implements the Grow-Shrink (GS) algorithm, the Incremental Association (IAMB) algorithm, the Interleaved-IAMB (Inter-IAMB) algorithm, the Fast-IAMB (Fast-IAMB) algorithm, the Max-Min Parents and Children (MMPC) algorithm and the Hill-Climbing (HC) greedy search algorithm for both discrete and Gaussian networks, along with many score functions and conditional independence tests. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as basic parametric and bootstrap inference functions.

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Package ouch updated to version 2.5-6 with previous version 2.5-4 dated 2009-03-13

Author: Aaron A. King and Marguerite A. Butler
Title: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses
Description: Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.

Diff between ouch versions 2.5-4 dated 2009-03-13 and 2.5-6 dated 2009-07-21

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More information about ouch at CRAN
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Package micEcon updated to version 0.5-22 with previous version 0.5-18 dated 2009-05-05

Author: Arne Henningsen
Title: Microeconomic Analysis and Modelling
Description: Tools for microeconomic analysis and microeconomic modelling

Diff between micEcon versions 0.5-18 dated 2009-05-05 and 0.5-22 dated 2009-07-21

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New package mixfdr with initial version 1.0
Package: mixfdr
Type: Package
Title: Computes false discovery rates and effect sizes using normal mixtures
Version: 1.0
Date: 2009-07-21
Author: Omkar Muralidharan, with many suggestions from Bradley Efron
Maintainer: Omkar Muralidharan
Description: This package fits normal mixture models to data and uses them to compute effect size estimates and local and tail area false discovery rates. To make this precise, suppose you have many normally distributed z's, and each z[i] has mean delta[i]. This package will estimate delta[i] based on the z's (effect sizes), P(delta[i]=0|z[i]) (local false discovery rates) and P(delta[i]=0||z[i]|>z) (tail area false discovery rates).
License: GPL-2
LazyLoad: yes
Packaged: Tue Jul 21 03:21:06 2009; omkar
Repository: CRAN
Date/Publication: 2009-07-21 15:17:46

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Package OrdMonReg updated to version 1.0.1 with previous version 1.0.0 dated 2009-04-15

Author: Fadoua Balabdaoui, Kaspar Rufibach, Filippo Santambrogio
Title: Compute least squares estimates of one bounded or two ordered isotonic regression curves
Description: We consider the problem of estimating two isotonic regression curves g1* and g2* under the constraint that they are ordered, i.e. g1* <= g2*. Given two sets of n data points y_1, ..., y_n and z_1, ..., z_n that are observed at (the same) deterministic design points x_1, ..., x_n, the estimates are obtained by minimizing the Least Squares criterion L(a, b) = sum_{i=1}^n (y_i - a_i)^2 w1(x_i) + sum_{i=1}^n (z_i - b_i)^2 w2(x_i) over the class of pairs of vectors (a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, ..., n. The estimates are computed with a projected subgradient algorithm where the projection is calculated using a PAVA.

Diff between OrdMonReg versions 1.0.0 dated 2009-04-15 and 1.0.1 dated 2009-07-21

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Package MasterBayes updated to version 2.44 with previous version 2.43 dated 2009-04-14

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.

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Package FactoClass updated to version 1.0.1 with previous version 0.7.7 dated 2009-05-06

Author: Campo Elias Pardo and Pedro Cesar del Campo , with the contributions from 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 0.7.7 dated 2009-05-06 and 1.0.1 dated 2009-07-21

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Permanent link

Package qpcR updated to version 1.2-0 with previous version 1.1-8 dated 2009-03-27

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).

Diff between qpcR versions 1.1-8 dated 2009-03-27 and 1.2-0 dated 2009-07-21

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Permanent link

New package sendmailR with initial version 1.0-0
Package: sendmailR
Version: 1.0-0
Title: send email from inside R
Description: Package contains a simple smtp client which provides a porable solution for sending emails from within R.
Author: Olaf Mersmann
Maintainer: Olaf Mersmann
Depends: R (>= 2.9.0)
License: GPL-2
LazyData: yes
Date:
Packaged: 2009-07-20 22:27:11 UTC; olafm
Repository: CRAN
Date/Publication: 2009-07-21 12:29:26

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New package sbr with initial version 0.1-1
Package: sbr
Version: 0.1-1
Date: 2009-07-01
Title: Safe Binary Regression
Author: Kjell Konis
Maintainer: Kjell Konis
Depends: R (>= 2.8.1), lpSolveAPI (>= 5.5.0.14)
LinkingTo: lpSolveAPI
Description: Overrides the glm function in the stats package so that a test for the existence of the maximum likelihood estimate is computed as part of the fitting procedure for binary regression models.
License: GPL-2
Packaged: 2009-07-20 13:41:22 UTC; konis
Repository: CRAN
Date/Publication: 2009-07-21 12:29:24

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Package plspm updated to version 0.1-4 with previous version 0.1-3 dated 2009-05-19

Author: Gaston Sanchez , and Laura Trinchera
Title: Partial Least Squares data analysis methods
Description: Partial Least Squares (PLS) methods with emphasis on structural equation models with latent variables.

Diff between plspm versions 0.1-3 dated 2009-05-19 and 0.1-4 dated 2009-07-21

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Package phangorn updated to version 0.99-2 with previous version 0.0-5 dated 2009-01-22

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 0.0-5 dated 2009-01-22 and 0.99-2 dated 2009-07-21

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New package pgs with initial version 0.2-0
Package: pgs
Version: 0.2-0
Date: June 2009
Title: Precision of Geometric Sampling
Description: Computation of mean squared errors of stereological predictors.
Author: Kien Kieu , Marianne Mora
Maintainer: Kien Kieu
Depends: methods, gsl, adapt
License: CeCILL
Encoding: latin1
Packaged: Tue Jul 21 09:09:38 2009; kien
Repository: CRAN
Date/Publication: 2009-07-21 12:28:48

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New package mstate with initial version 0.2.1
Package: mstate
Version: 0.2.1
Date: 2009-07-10
Title: Data preparation, estimation and prediction in multi-state models
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco
Maintainer: Hein Putter
Depends: survival
Imports: survival
Suggests: cmprsk
Description: Functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models
License: GPL (>= 2)
URL: http://www.msbi.nl/putter
Packaged: 2009-07-20 09:02:14 UTC; hputter
Repository: CRAN
Date/Publication: 2009-07-21 12:28:43

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Package lawstat updated to version 2.3 with previous version 2.2 dated 2007-11-14

Author: Kimihiro Noguchi , W. L. Wallace Hui , Yulia R. Gel , Joseph L. Gastwirth , Weiwen Miao
Title: An R package for biostatistics, public policy, and law
Description: An R software package on statistical tests widely utilized in biostatistics, public policy and law. Along with the well known tests for equality of means and variances, randomness, measures of relative variability etc, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.

Diff between lawstat versions 2.2 dated 2007-11-14 and 2.3 dated 2009-07-21

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Package gamlss.tr updated to version 3.0-0 with previous version 2.0-0 dated 2009-04-03

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 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21

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

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Permanent link

Package gamlss.nl updated to version 3.0-0 with previous version 2.0-0 dated 2009-04-03

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 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21

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

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Permanent link

Package gamlss.mx updated to version 3.0-0 with previous version 2.0-0 dated 2009-04-03

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 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21

 DESCRIPTION           |    8 ++++----
 R/gamlssMX-10-11-07.R |   18 ++++++++++++++++--
 2 files changed, 20 insertions(+), 6 deletions(-)

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Permanent link

Package gamlss.dist updated to version 3.0-0 with previous version 2.0-0 dated 2009-04-03

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 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21

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Permanent link

New package gamlss.data with initial version 3.0-0
Package: gamlss.data
Description: Data for GAMLSS models.
Title: GAMLSS Data.
LazyLoad: yes
Version: 3.0-0
Date: 2008-07-14
Depends: R (>= 2.4.0)
Author: Mikis Stasinopoulos , Bob Rigby
Maintainer: Mikis Stasinopoulos
License: GPL-2 | GPL-3
URL: http://www.gamlss.com/
Packaged: 2009-07-14 17:08:40 UTC; stasinom
Repository: CRAN
Date/Publication: 2009-07-21 12:22:37

More information about gamlss.data at CRAN
Permanent link

Package gamlss.cens updated to version 3.0.0 with previous version 2.0.0 dated 2009-04-03

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 2.0.0 dated 2009-04-03 and 3.0.0 dated 2009-07-21

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

More information about gamlss.cens at CRAN
Permanent link

Package gamlss updated to version 3.0-0 with previous version 2.0-0 dated 2009-04-03

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 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21

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More information about gamlss at CRAN
Permanent link

Package bear updated to version 2.4.0 with previous version 2.3.1 dated 2009-04-14

Author: Hsin-ya Lee , Yung-jin Lee
Title: Average bioequivalence and bioavailability data analysis tool
Description: An average bioequivalence (ABE) and bioavailability data analysis tool including sample size estimation, noncompartmental analysis (NCA), ANOVA (lm) for a standard RT/TR 2x2x2 crossover design and linear mixed effect model (lme of nlme) for a 2-treatment, 2-sequence, with 2 periods or more (i.e. 2x2x3/2x2x4) replicate design or a 2-treatment, 2-sequence, and 1-period parallel ABE study (2x2x1).

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Package ape updated to version 2.3-2 with previous version 2.3-1 dated 2009-06-24

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, the population parameter theta based on various approaches, nucleotide diversity, 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 2.3-1 dated 2009-06-24 and 2.3-2 dated 2009-07-21

 ChangeLog           |   24 ++++
 DESCRIPTION         |    8 -
 R/all.equal.phylo.R |   34 +++--
 R/chronopl.R        |   39 +++---
 R/dist.topo.R       |   16 +-
 R/drop.tip.R        |    4 
 R/nj.R              |   16 +-
 R/root.R            |   25 ++--
 R/vcv.phylo.R       |    3 
 Thanks              |    4 
 inst/doc/MoranI.pdf |binary
 src/nj.c            |  309 ++++++++++++++++++++++------------------------------
 12 files changed, 241 insertions(+), 241 deletions(-)

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Package MSBVAR updated to version 0.4.0 with previous version 0.3.2 dated 2008-10-12

Author: Patrick T. Brandt
Title: Markov-Switching, Bayesian, Vector Autoregression Models
Description: Provides methods for estimating frequentist and Bayesian Vector Autoregression (VAR) models. Functions for reduced form and structural VAR models are also available. Includes methods for the generating posterior inferences for VAR forecasts, impulse responses (using likelihood-based error bands), and forecast error decompositions. Also includes utility functions for plotting forecasts and impulse responses, and generating draws from Wishart and singular multivariate normal densities. Current version includes some limited functionality to build models with Markov switching.

Diff between MSBVAR versions 0.3.2 dated 2008-10-12 and 0.4.0 dated 2009-07-21

 DESCRIPTION                |   33 ++++++++++++++++++---------------
 INDEX                      |   21 +++++++++++++++++++++
 LICENSE                    |    6 +++---
 NAMESPACE                  |   28 +++++++++++++++++++++++++---
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 README                     |   39 ++++++++++++++++++++++++++++-----------
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 man/SZ.prior.evaluation.Rd |    5 +++--
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 51 files changed, 277 insertions(+), 165 deletions(-)

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New package ReacTran with initial version 1.1
Package: ReacTran
Version: 1.1
Title: Reactive transport modelling in 1D, 2D and 3D
Author: Karline Soetaert , Filip Meysman
Maintainer: Karline Soetaert
Depends: R (>= 2.01), rootSolve, deSolve, shape
Description: Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions. Includes transport routines in porous media, in estuaries, and in bodies with variable shape.
License: GPL
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: reactran
Repository/R-Forge/Revision: 47
Date/Publication: 2009-07-21 12:27:08
Packaged: 2009-07-19 20:24:32 UTC; rforge

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Package COZIGAM updated to version 2.0-2 with previous version 2.0-1 dated 2009-02-25

Author: Hai Liu , Kung-Sik Chan
Title: Constrained and Unconstrained Zero-Inflated Generalized Additive Models with Model Selection Criterion
Description: Constrained and Unconstrained Zero-Inflated Generalized Additive Models (ZIGAM) fitting with associated model plotting, prediction and selection.

Diff between COZIGAM versions 2.0-1 dated 2009-02-25 and 2.0-2 dated 2009-07-21

 DESCRIPTION            |   21 +++++++++++++--------
 R/cozigam.R            |   32 +++++++++++++++++++-------------
 man/COZIGAM-package.rd |only
 man/alaska.rd          |   10 ++++++----
 man/eggdata.rd         |   17 +++++++++--------
 5 files changed, 47 insertions(+), 33 deletions(-)

More information about COZIGAM at CRAN
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