CRANberries

CRANberries aggregates information about new and and updated packages from the
CRAN network for R available as this html version and a corresponding RSS feed.
Created and provided by Dirk Eddelbuettel.

Wed, 27 Jan 2010

Package randomSurvivalForest updated to version 3.6.1 with previous version 3.6.0 dated 2009-12-21

Title: Ishwaran and Kogalur's Random Survival Forest
Description: Ensemble survival analysis based on a random forest of trees using random inputs.
Author: Hemant Ishwaran , Udaya B. Kogalur
Maintainer: Udaya B. Kogalur

Diff between randomSurvivalForest versions 3.6.0 dated 2009-12-21 and 3.6.1 dated 2010-01-27

 DESCRIPTION              |    8 ++++----
 R/competing.risk.R       |    2 +-
 R/extract.factor.R       |    2 +-
 R/find.interaction.R     |    2 +-
 R/impute.rsf.R           |    2 +-
 R/max.subtree.R          |    2 +-
 R/plot.ensemble.R        |    2 +-
 R/plot.error.R           |    2 +-
 R/plot.proximity.R       |    2 +-
 R/plot.rsf.R             |    2 +-
 R/plot.variable.R        |    2 +-
 R/pmml2rsf.R             |    2 +-
 R/predict.rsf.R          |    2 +-
 R/print.rsf.R            |    2 +-
 R/randomSurvivalForest.R |    2 +-
 R/rsf.R                  |    2 +-
 R/rsf.default.R          |    2 +-
 R/rsf.formula.R          |    2 +-
 R/rsf.news.R             |    2 +-
 R/rsf2pmml.R             |    2 +-
 R/rsf2rfz.R              |    2 +-
 R/varSel.R               |    2 +-
 R/vimp.R                 |    2 +-
 R/zzz.R                  |    2 +-
 inst/NEWS                |   32 +++++++++++++++++++++-----------
 src/extern.h             |    4 ++--
 src/factor.h             |    2 +-
 src/global.h             |    2 +-
 src/node.h               |    2 +-
 src/nodeOps.c            |    2 +-
 src/nodeOps.h            |    2 +-
 src/nrutil.c             |    2 +-
 src/nrutil.h             |    2 +-
 src/rsf.c                |   10 +++++-----
 src/rsf.h                |    2 +-
 src/rsfBootstrap.c       |    2 +-
 src/rsfBootstrap.h       |    2 +-
 src/rsfEntry.c           |    4 ++--
 src/rsfEntry.h           |    2 +-
 src/rsfFactorOps.c       |    2 +-
 src/rsfFactorOps.h       |    2 +-
 src/rsfImportance.c      |    6 +++---
 src/rsfImportance.h      |    2 +-
 src/rsfImpute.c          |    8 ++++----
 src/rsfImpute.h          |    2 +-
 src/rsfSplit.c           |    2 +-
 src/rsfSplit.h           |    2 +-
 src/rsfSplitUtil.c       |    2 +-
 src/rsfSplitUtil.h       |    2 +-
 src/rsfStack.c           |   38 +++++++++++++++++++-------------------
 src/rsfStack.h           |    2 +-
 src/rsfTree.c            |    2 +-
 src/rsfTree.h            |    2 +-
 src/rsfUtil.c            |    4 ++--
 src/rsfUtil.h            |    2 +-
 src/trace.c              |    2 +-
 src/trace.h              |    2 +-
 57 files changed, 110 insertions(+), 100 deletions(-)

More information about randomSurvivalForest at CRAN
Path: /cran/updated | permanent link

New package trio with initial version 1.0.2
Package: trio
Type: Package
Title: Processing and Simulating Genotype Data for Trio Logic Regression
Version: 1.0.2
Date: 2010-02-26
Author: Qing Li, Holger Schwender
Maintainer: Qing Li
Depends: survival, haplo.stats
Description: Set up matched case-pseudo controls genotypes data for trios in order to run trio logic regreesion, to impute missing genotypes in trios, or to simulate case-parent trios with disease risk dependent on SNP-SNP interaction. This package furthermore contains functions for computing the values of pairwise LD measures and for identifying LD blocks.
License: LGPL-2
Packaged: 2010-01-26 23:26:57 UTC; hschwend
Repository: CRAN
Date/Publication: 2010-01-27 16:30:45

More information about trio at CRAN
Path: /cran/new | permanent link

Package party updated to version 0.9-9991 with previous version 0.9-999 dated 2009-09-24

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available.
Author: Torsten Hothorn, Kurt Hornik, Carolin Strobl and Achim Zeileis
Maintainer: Torsten Hothorn

Diff between party versions 0.9-999 dated 2009-09-24 and 0.9-9991 dated 2010-01-27

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 party-0.9-999/party/inst/documentation/man                                                                    |only
 party-0.9-9991/party/DESCRIPTION                                                                              |    8 
 party-0.9-9991/party/NEWS                                                                                     |    4 
 party-0.9-9991/party/R/MOB-Utils.R                                                                            |   16 
 party-0.9-9991/party/cleanup                                                                                  |    3 
 party-0.9-9991/party/inst/doc/MOB.Rnw                                                                         |   12 
 party-0.9-9991/party/inst/doc/MOB.pdf                                                                         |  928 ++--
 party-0.9-9991/party/inst/doc/party.Rnw                                                                       |   12 
 party-0.9-9991/party/inst/doc/party.pdf                                                                       |binary
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Path: /cran/updated | permanent link

Package BioIDMapper updated to version 2.0 with previous version 1.2 dated 2009-09-04

Title: Mapping between BioIDs
Description: facilitate mapping between different databases, integrate various ID systems and provide a full view from gene level, mRNA level and functional level regarding one specific ID. The mapping system is based on NCBI and UniProt web service.
Author: Xiaoyong Sun
Maintainer: Xiaoyong Sun

Diff between BioIDMapper versions 1.2 dated 2009-09-04 and 2.0 dated 2010-01-27

 DESCRIPTION              |   14 ++--
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 15 files changed, 196 insertions(+), 37 deletions(-)

More information about BioIDMapper at CRAN
Path: /cran/updated | permanent link

Package timereg updated to version 1.2-9 with previous version 1.2-7 dated 2009-11-26

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, semiparametric proportional odds model, cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS and Lasso for the additive risk model.
Author: Thomas Scheike with contributions from Torben Martinussen and Jeremy Silver
Maintainer: Thomas Scheike

Diff between timereg versions 1.2-7 dated 2009-11-26 and 1.2-9 dated 2010-01-27

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 12 files changed, 355 insertions(+), 285 deletions(-)

More information about timereg at CRAN
Path: /cran/updated | permanent link

Package rgrs updated to version 0.2-15 with previous version 0.2-14 dated 2009-08-25

Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social sciences students or researchers. Currently it includes functions for cross-tabulation, weighting, results export, and maps plotting. The documentation and help pages are written in french.
Author: Julien Barnier
Maintainer: Julien Barnier

Diff between rgrs versions 0.2-14 dated 2009-08-25 and 0.2-15 dated 2010-01-27

 DESCRIPTION                 |   14 +++++++-------
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More information about rgrs at CRAN
Path: /cran/updated | permanent link

Package qAnalyst updated to version 0.6.1 with previous version 0.6.0 dated 2009-08-23

Title: Control Charts, Capability and Distribution Identification
Description: qAnalyst performs: control charts for variables and attributes according to Douglas C. Montgomery Introduction to Statistical Quality Control book, Capability analysis for normal and non - normal distributions and Distributions Identification
Author: Andrea Spano'
Maintainer: Andrea Spano'

Diff between qAnalyst versions 0.6.0 dated 2009-08-23 and 0.6.1 dated 2010-01-27

 DESCRIPTION         |    8 -
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More information about qAnalyst at CRAN
Path: /cran/updated | permanent link

Package mvtnorm updated to version 0.9-9 with previous version 0.9-8 dated 2009-10-27

Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch, Fabian Scheipl, Torsten Hothorn
Maintainer: Torsten Hothorn

Diff between mvtnorm versions 0.9-8 dated 2009-10-27 and 0.9-9 dated 2010-01-27

 DESCRIPTION            |    8 ++++----
 NEWS                   |    4 ++++
 R/mvnorm.R             |    3 ++-
 inst/CHANGES           |    4 ++++
 inst/doc/MVT_Rnews.pdf |binary
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 7 files changed, 18 insertions(+), 7 deletions(-)

More information about mvtnorm at CRAN
Path: /cran/updated | permanent link

Package lmPerm updated to version 1.0-1 with previous version 1.0-0 dated 2010-01-26

Title: Permutation tests for linear models
Description: Linear model functions using permutation tests.
Author: Bob Wheeler
Maintainer: Bob Wheeler

Diff between lmPerm versions 1.0-0 dated 2010-01-26 and 1.0-1 dated 2010-01-27

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More information about lmPerm at CRAN
Path: /cran/updated | permanent link

Package coin updated to version 1.0-10 with previous version 1.0-9 dated 2009-12-30

Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.
Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim Zeileis
Maintainer: Torsten Hothorn

Diff between coin versions 1.0-9 dated 2009-12-30 and 1.0-10 dated 2010-01-27

 coin-1.0-10/coin/DESCRIPTION                                                                              |    8 
 coin-1.0-10/coin/NEWS                                                                                     |    6 
 coin-1.0-10/coin/R/ExactDistributions.R                                                                   |   21 
 coin-1.0-10/coin/inst/doc/LegoCondInf.pdf                                                                 |binary
 coin-1.0-10/coin/inst/doc/MAXtest.pdf                                                                     |binary
 coin-1.0-10/coin/inst/doc/coin.pdf                                                                        |binary
 coin-1.0-10/coin/inst/doc/coin_implementation.pdf                                                         |binary
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 coin-1.0-10/coin/inst/documentation/html/index.html                                                       |   15 
 coin-1.0-10/coin/inst/documentation/html/main.html                                                        |   23 
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 coin-1.0-10/coin/inst/documentation/html/tabs.css                                                         |    2 
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 coin-1.0-10/coin/inst/documentation/man/man3/celW.3                                                       |    2 
 coin-1.0-10/coin/inst/documentation/man/man3/coin_common.h.3                                              |    2 
 coin-1.0-10/coin/inst/documentation/man/man3/vandeWiel.c.3                                                |    4 
 coin-1.0-10/coin/man/ExactNullDistribution-methods.Rd                                                     |    5 
 coin-1.0-10/coin/man/IndependenceLinearStatistic-class.Rd                                                 |   22 
 coin-1.0-10/coin/man/IndependenceTestStatistic-class.Rd                                                   |   26 
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 coin-1.0-10/coin/man/ScalarIndependenceTestStatistic-class.Rd                                             |   28 
 coin-1.0-10/coin/man/initialize-methods.Rd                                                                |   26 
 coin-1.0-10/coin/man/show-methods.Rd                                                                      |   10 
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 coin-1.0-10/coin/tests/bugfixes.Rout.save                                                                 |    2 
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 coin-1.0-10/coin/tests/comparisons.Rout.save                                                              |    2 
 coin-1.0-10/coin/tests/regtest_2sample.Rout.save                                                          |    2 
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 coin-1.0-10/coin/tests/regtest_MTP.Rout.save                                                              |  638 +++++-----
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More information about coin at CRAN
Path: /cran/updated | permanent link

Package sp updated to version 0.9-57 with previous version 0.9-56 dated 2010-01-13

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

Diff between sp versions 0.9-56 dated 2010-01-13 and 0.9-57 dated 2010-01-27

 ChangeLog                           |   65 +
 DESCRIPTION                         |   10 
 R/GridTopology-methods.R            |    2 
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More information about sp at CRAN
Path: /cran/updated | permanent link

Package simone updated to version 0.1-4 with previous version 0.1-3 dated 2009-05-28

Title: Statistical Inference for MOdular NEtworks (SIMoNe)
Description: The SIMoNe algorithm iteratively combines edge estimation and node classification on the basis of a mixture model for edge weight distributions. Edges inference may be managed via two alternative methods: GLasso and Meinhausan-Buhlman's approach. Node Classification is managed by MixNet, a mixture model for random graphs.
Author: Christophe Ambroise , Julien Chiquet , Gilles Grasseau , Alexander Adam Smith
Maintainer: Gilles Grasseau

Diff between simone versions 0.1-3 dated 2009-05-28 and 0.1-4 dated 2010-01-27

 DESCRIPTION  |    8 ++++----
 NEWS         |    4 ++++
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 3 files changed, 11 insertions(+), 7 deletions(-)

More information about simone at CRAN
Path: /cran/updated | permanent link

Package rpartOrdinal updated to version 2.0 with previous version 1.1 dated 2009-11-03

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.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer

Diff between rpartOrdinal versions 1.1 dated 2009-11-03 and 2.0 dated 2010-01-27

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More information about rpartOrdinal at CRAN
Path: /cran/updated | permanent link

Package rainbow updated to version 1.8 with previous version 1.7 dated 2009-12-20

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

Diff between rainbow versions 1.7 dated 2009-12-20 and 1.8 dated 2010-01-27

 CHANGELOG       |   46 ++++++++++++++++++++++++++++++----------------
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More information about rainbow at CRAN
Path: /cran/updated | permanent link

Package phangorn updated to version 0.99-6 with previous version 0.99-5 dated 2010-01-15

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)
Author: Klaus Schliep
Maintainer: Klaus Schliep

Diff between phangorn versions 0.99-5 dated 2010-01-15 and 0.99-6 dated 2010-01-27

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More information about phangorn at CRAN
Path: /cran/updated | permanent link

Package mlogit updated to version 0.1-4 with previous version 0.1-3 dated 2010-01-26

Title: multinomial logit model
Description: Estimation of the multinomial logit model with choice specific variables
Author: Yves Croissant
Maintainer: Yves Croissant

Diff between mlogit versions 0.1-3 dated 2010-01-26 and 0.1-4 dated 2010-01-27

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More information about mlogit at CRAN
Path: /cran/updated | permanent link

Package mixer updated to version 1.2 with previous version 1.1 dated 2009-11-27

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

Diff between mixer versions 1.1 dated 2009-11-27 and 1.2 dated 2010-01-27

 DESCRIPTION  |    8 ++++----
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More information about mixer at CRAN
Path: /cran/updated | permanent link

Package filehash updated to version 2.0-2 with previous version 2.0-1 dated 2008-12-21

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

Diff between filehash versions 2.0-1 dated 2008-12-21 and 2.0-2 dated 2010-01-27

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More information about filehash at CRAN
Path: /cran/updated | permanent link

New package exactci with initial version 1.0-0
Package: exactci
Type: Package
Title: Exact P-values and Matching Confidence Intervals for simple Discrete Parametric Cases
Version: 1.0-0
Date: 2010-01-04
Author: M.P. Fay
Maintainer: M.P. Fay
Depends: stats
Description: Calculates exact tests and confidence intervals for one and two-sample binomial and Poisson cases.
License: GPL-2
LazyLoad: yes
Packaged: 2010-01-26 20:38:31 UTC; faym
Repository: CRAN
Date/Publication: 2010-01-27 10:51:25

More information about exactci at CRAN
Path: /cran/new | permanent link

Package exact2x2 updated to version 1.0-0 with previous version 0.9-3.1 dated 2009-08-14

Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals.
Author: M.P. Fay
Maintainer: M.P. Fay

Diff between exact2x2 versions 0.9-3.1 dated 2009-08-14 and 1.0-0 dated 2010-01-27

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More information about exact2x2 at CRAN
Path: /cran/updated | permanent link

Package clusterSim updated to version 0.37-1 with previous version 0.36-6 dated 2009-10-23

Title: Searching for optimal clustering procedure for a data set
Description: GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication analysis for cluster validation, Clustering with several algorithms, distances, normalizations and icq indices, Symbolic interval distances, Plot functions, Random cluster generation
Author: Marek Walesiak Andrzej Dudek
Maintainer: Andrzej Dudek

Diff between clusterSim versions 0.36-6 dated 2009-10-23 and 0.37-1 dated 2010-01-27

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More information about clusterSim at CRAN
Path: /cran/updated | permanent link

Package ElectroGraph updated to version 0.2.0 with previous version 0.1.1 dated 2010-01-15

Title: Enhanced routines for plotting and analyzing valued relational data.
Description: This package contains routines and procedures for relational data, namely considerations for valued ties. In particular, relative distances are calculated using social conductance methods.
Author: Andrew C. Thomas
Maintainer: Andrew C. Thomas

Diff between ElectroGraph versions 0.1.1 dated 2010-01-15 and 0.2.0 dated 2010-01-27

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More information about ElectroGraph at CRAN
Path: /cran/updated | permanent link

Package DPpackage updated to version 1.0-9 with previous version 1.0-8 dated 2009-10-20

Title: Bayesian Nonparametric and Semiparametric Analysis
Description: This package contains functions to perform inference via simulation from the posterior distributions for Bayesian nonparametric and semiparametric models. Although the name of the package was motivated by the Dirichlet Process prior, the package considers and will consider other priors on functional spaces. So far, DPpackage includes models considering Dirichlet Processes, Dependent Dirichlet Processes, Dependent Poisson- Dirichlet Processes, Hierarchical Dirichlet Processes, Polya Trees, Mixtures of Triangular distributions, and Random Bernstein polynomials priors. The package also includes models considering Penalized B-Splines. Currently the package includes semiparametric models for marginal and conditional density estimation, ROC curve analysis, interval censored data, binary regression models, generalized linear mixed models, IRT type models, and generalized additive models. The package also contains functions to compute Pseudo-Bayes factors for model comparison, and to elicitate the precision parameter of the Dirichlet Process. To maximize computational efficiency, the actual sampling for each model is done in compiled FORTRAN. The functions return objects which can be subsequently analyzed with functions provided in the coda package.
Author: Alejandro Jara with contributions from Timothy Hanson , Fernando A. Quintana , Peter Mueller , and Gary L. Rosner .
Maintainer: Alejandro Jara

Diff between DPpackage versions 1.0-8 dated 2009-10-20 and 1.0-9 dated 2010-01-27

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 129 files changed, 2151 insertions(+), 1686 deletions(-)

More information about DPpackage at CRAN
Path: /cran/updated | permanent link

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