Tue, 31 Mar 2009

New package AquaEnv with initial version 0.7
Package: AquaEnv
Version: 0.7
Date: 2009-03-24
Title: AquaEnv - an integrated development toolbox for aquatic chemical model generation
Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Maintainer: Andreas F. Hofmann
Depends: minpack.lm, deSolve, seacarb
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.
License: GPL (>= 2)
LazyData: yes
Packaged: Tue Mar 31 12:30:54 2009; andreash
Repository: CRAN
Date/Publication: 2009-03-31 18:25:59

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Package sp updated to version 0.9-34 with previous version 0.9-32 dated 2009-02-20

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 0.9-32 dated 2009-02-20 and 0.9-34 dated 2009-03-31

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Package cluster updated to version 1.11.13 with previous version 1.11.12 dated 2009-01-07

Author: Martin Maechler, based on S original by Peter Rousseeuw , Anja.Struyf@uia.ua.ac.be and Mia.Hubert@uia.ua.ac.be, and initial R port by Kurt.Hornik@R-project.org
Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis, extended original from Peter Rousseeuw, Anja Struyf and Mia Hubert.

Diff between cluster versions 1.11.12 dated 2009-01-07 and 1.11.13 dated 2009-03-31

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Package WriteXLS updated to version 1.6.0 with previous version 1.5.0 dated 2009-03-26

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.

Diff between WriteXLS versions 1.5.0 dated 2009-03-26 and 1.6.0 dated 2009-03-31

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Package Matrix updated to version 0.999375-23 with previous version 0.999375-22 dated 2009-03-13

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 0.999375-22 dated 2009-03-13 and 0.999375-23 dated 2009-03-31

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Package proxy updated to version 0.4-2 with previous version 0.4-1 dated 2008-08-29

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 0.4-1 dated 2008-08-29 and 0.4-2 dated 2009-03-31

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Package StatDataML updated to version 1.0-17 with previous version 1.0-16 dated 2009-02-05

Author: David Meyer , Torsten Hothorn , Friedrich Leisch
Title: implementation of the StatDataML proposal
Description: read and write StatDataML files

Diff between StatDataML versions 1.0-16 dated 2009-02-05 and 1.0-17 dated 2009-03-31

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Package Rglpk updated to version 0.2-9 with previous version 0.2-8 dated 2009-02-07

Author: Stefan Theussl and Kurt Hornik
Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programing Kit (GLPK version 4.37). GLPK is open source software for solving large-scale linear programming (LP), mixed integer linear programming (MILP) and other related problems.

Diff between Rglpk versions 0.2-8 dated 2009-02-07 and 0.2-9 dated 2009-03-31

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Package graphicsQC updated to version 1.0-3 with previous version 1.0-2 dated 2009-02-11

Author: Stephen Gardiner and Paul Murrell
Title: Quality Control for Graphics in R
Description: The package provides functions to generate graphics files, compare them with ``model'' files, and report the results.

Diff between graphicsQC versions 1.0-2 dated 2009-02-11 and 1.0-3 dated 2009-03-31

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Package epiR updated to version 0.9-15 with previous version 0.9-14 dated 2008-12-19

Author: Mark Stevenson with contributions from Telmo Nunes, Javier Sanchez, and Ron Thornton.
Title: Functions for analysing epidemiological data
Description: A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.

Diff between epiR versions 0.9-14 dated 2008-12-19 and 0.9-15 dated 2009-03-31

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Mon, 30 Mar 2009

Package timereg updated to version 1.1-7 with previous version 1.1-6 dated 2009-02-11

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.

Diff between timereg versions 1.1-6 dated 2009-02-11 and 1.1-7 dated 2009-03-30

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Package rPorta updated to version 0.1-9 with previous version 0.1-8 dated 2009-02-03

Author: Robin Nunkesser , Silke Straatmann, Simone Wenzel
Title: R/PORTA interface
Description: An R interface to a modified version of PORTA. For more information on PORTA see http://www.zib.de/Optimization/Software/Porta/.

Diff between rPorta versions 0.1-8 dated 2009-02-03 and 0.1-9 dated 2009-03-30

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Package grplasso updated to version 0.4-1 with previous version 0.3-2 dated 2009-02-11

Author: Lukas Meier
Title: Fitting user specified models with Group Lasso penalty
Description: Fits user specified (GLM-) models with Group Lasso penalty

Diff between grplasso versions 0.3-2 dated 2009-02-11 and 0.4-1 dated 2009-03-30

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Package untb updated to version 1.4-2 with previous version 1.3-3 dated 2009-01-20

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.

Diff between untb versions 1.3-3 dated 2009-01-20 and 1.4-2 dated 2009-03-30

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Package magic updated to version 1.4-4 with previous version 1.4-3 dated 2009-01-22

Author: Robin K. S. Hankin
Title: create and investigate magic squares
Description: a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays. The package includes methods for creating normal magic squares of any order greater than 2. The ultimate intention is for the package to be a computerized embodiment all magic square knowledge, including direct numerical verification of properties of magic squares (such as recent results on the determinant of odd-ordered semimagic squares). Some antimagic functionality is included. The package also serves as a rebuttal to the often-heard comment "I thought R was just for statistics".

Diff between magic versions 1.4-3 dated 2009-01-22 and 1.4-4 dated 2009-03-30

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New package qtlbook with initial version 0.16-3
Package: qtlbook
Version: 0.16-3
Date: 29 March 2009
Title: Datasets for the R/qtl book
Author: Karl W Broman
Maintainer: Karl W Broman
Description: Datasets for the book, A guide to QTL Mapping with R/qtl
Depends: qtl
License: GPL (>= 2)
URL: http://www.rqtl.org/book
Packaged: Sun Mar 29 15:34:35 2009; kbroman
Repository: CRAN
Date/Publication: 2009-03-30 06:47:05

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Package gsl updated to version 1.8-13 with previous version 1.8-11 dated 2008-08-22

Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and multimin by Andrew Clausen
Title: wrapper for the Gnu Scientific Library
Description: An R wrapper for the special functions and quasi random number generators of the Gnu Scientific Library (http://www.gnu.org/software/gsl/). See gsl-package.Rd for details of overall package organization, and Misc.Rd for some functions that are widely used in the package.

Diff between gsl versions 1.8-11 dated 2008-08-22 and 1.8-13 dated 2009-03-30

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Package denstrip updated to version 1.3 with previous version 1.2 dated 2008-11-03

Author: Christopher Jackson
Title: Density strips and other methods for compactly illustrating distributions
Description: Graphical methods for compactly illustrating probability distributions, including density strips, density regions, sectioned density plots and varying width strips.

Diff between denstrip versions 1.2 dated 2008-11-03 and 1.3 dated 2009-03-30

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Package ape updated to version 2.3 with previous version 2.2-4 dated 2009-02-09

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, classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

Diff between ape versions 2.2-4 dated 2009-02-09 and 2.3 dated 2009-03-30

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Sun, 29 Mar 2009

Package maptools updated to version 0.7-21 with previous version 0.7-20 dated 2009-02-18

Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko, Stéphane Dray, David Forrest, Patrick Giraudoux, Duncan Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Thomas Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai and Tom Short
Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHS shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.

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New package tmvtnorm with initial version 0.4-2
Package: tmvtnorm
Version: 0.4-2
Date: 2009-03-29
Title: Truncated Multivariate Normal Distribution
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
Imports: stats, graphics
Depends: R (>= 1.9.0), mvtnorm, utils
Description: Computes truncated multivariate normal probabilities, quantiles and densities, including one-dimensional marginal densities
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2009-03-29 16:53:41 UTC; stefan
Repository: CRAN
Date/Publication: 2009-03-29 18:09:54

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Package tuneR updated to version 0.2-10 with previous version 0.2-8 dated 2009-01-09

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 0.2-8 dated 2009-01-09 and 0.2-10 dated 2009-03-29

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 man/equalWave.Rd   |    2 +-
 man/extractWave.Rd |    2 +-
 man/noSilence.Rd   |    2 +-
 man/normalize.Rd   |    2 +-
 man/panorama.Rd    |    2 +-
 man/periodogram.Rd |    2 +-
 man/play.Rd        |    2 +-
 man/plot-Wave.Rd   |    2 +-
 man/prepComb.Rd    |    2 +-
 man/show.Rd        |    2 +-
 man/summary.Rd     |    2 +-
 25 files changed, 43 insertions(+), 54 deletions(-)

More information about tuneR at CRAN
Permanent link

Package qtl updated to version 1.11-12 with previous version 1.10-27 dated 2009-01-11

Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Brian Yandell
Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

Diff between qtl versions 1.10-27 dated 2009-01-11 and 1.11-12 dated 2009-03-29

 .gitignore              |only
 DESCRIPTION             |   18 +-
 R/add.cim.covar.R       |   14 +
 R/add_threshold.R       |   14 +
 R/addqtl.R              |   22 ++
 R/argmax.geno.R         |   14 +
 R/arithscan.R           |   14 +
 R/calc.genoprob.R       |   14 +
 R/calc.pairprob.R       |   14 +
 R/cim.R                 |   14 +
 R/compareorder.R        |   14 +
 R/countXO.R             |   14 +
 R/discan.R              |   14 +
 R/effectplot.R          |   90 +++++++++--
 R/effectscan.R          |   14 +
 R/errorlod.R            |   14 +
 R/est.map.R             |   14 +
 R/est.rf.R              |   14 +
 R/fitqtl.R              |   20 ++
 R/fitstahl.R            |   14 +
 R/makeqtl.R             |   66 +++++---
 R/map_construction.R    |   14 +
 R/plot.R                |  120 +++++++++++----
 R/plot.scanone.R        |   14 +
 R/plot.scantwo.R        |   14 +
 R/plotModel.R           |   14 +
 R/plotperm.R            |   14 +
 R/qtlcart_io.R          |   14 +
 R/read.cross.R          |   14 +
 R/read.cross.csv.R      |   14 +
 R/read.cross.csvs.R     |   14 +
 R/read.cross.gary.R     |   14 +
 R/read.cross.karl.R     |   14 +
 R/read.cross.mm.R       |   14 +
 R/read.cross.qtx.R      |   14 +
 R/refineqtl.R           |   14 +
 R/replacemap.R          |   14 +
 R/ripple.R              |   14 +
 R/scanone.R             |   14 +
 R/scanoneboot.R         |   14 +
 R/scanqtl.R             |   14 +
 R/scantwo.R             |   14 +
 R/sim.geno.R            |   14 +
 R/sim_ril.R             |   14 +
 R/simulate.R            |   14 +
 R/stepwiseqtl.R         |   14 +
 R/summary.cross.R       |   14 +
 R/summary.scanone.R     |   14 +
 R/summary.scantwo.R     |   14 +
 R/summary.scantwo.old.R |   14 +
 R/tryallpositions.R     |   14 +
 R/util.R                |  128 +++++++++++++++-
 R/vbscan.R              |   14 +
 R/write.cross.R         |   24 ++-
 R/xchr.R                |   14 +
 R/zzz.R                 |   14 +
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 inst/LICENSE.txt        |  384 +-----------------------------------------------
 inst/README.txt         |   12 -
 inst/STATUS.txt         |   71 ++++++++
 inst/TODO.txt           |    9 +
 inst/docs/rqtltour.R    |    4 
 inst/docs/rqtltour.pdf  |binary
 inst/docs/rqtltour.tex  |    4 
 man/effectplot.Rd       |    9 +
 man/qtl-internal.Rd     |    4 
 man/replaceqtl.Rd       |   10 -
 src/countXO.c           |   13 +
 src/countXO.h           |   13 +
 src/discan.c            |   13 +
 src/discan.h            |   13 +
 src/discan_covar.c      |   13 +
 src/discan_covar.h      |   13 +
 src/effectscan.c        |   13 +
 src/effectscan.h        |   13 +
 src/fitqtl_hk.c         |   13 +
 src/fitqtl_hk.h         |   13 +
 src/fitqtl_imp.c        |   13 +
 src/fitqtl_imp.h        |   13 +
 src/forwsel.c           |   13 +
 src/forwsel.h           |   13 +
 src/hmm_4way.c          |   13 +
 src/hmm_4way.h          |   13 +
 src/hmm_bc.c            |   13 +
 src/hmm_bc.h            |   13 +
 src/hmm_bci.c           |   13 +
 src/hmm_bci.h           |   13 +
 src/hmm_cc.c            |   13 +
 src/hmm_cc.h            |   13 +
 src/hmm_f2.c            |   13 +
 src/hmm_f2.h            |   13 +
 src/hmm_f2i.c           |   13 +
 src/hmm_f2i.h           |   13 +
 src/hmm_main.c          |   13 +
 src/hmm_main.h          |   13 +
 src/info.c              |   13 +
 src/info.h              |   13 +
 src/lapackutil.c        |   13 +
 src/lapackutil.h        |   13 +
 src/ripple.c            |   13 +
 src/ripple.h            |   13 +
 src/scanone_ehk.c       |   13 +
 src/scanone_ehk.h       |   13 +
 src/scanone_em.c        |   13 +
 src/scanone_em.h        |   13 +
 src/scanone_em_covar.c  |   13 +
 src/scanone_em_covar.h  |   13 +
 src/scanone_hk.c        |   13 +
 src/scanone_hk.h        |   13 +
 src/scanone_imp.c       |   13 +
 src/scanone_imp.h       |   13 +
 src/scanone_mr.c        |   13 +
 src/scanone_mr.h        |   13 +
 src/scanone_np.c        |   13 +
 src/scanone_np.h        |   13 +
 src/scantwo_binary_em.c |   13 +
 src/scantwo_binary_em.h |   13 +
 src/scantwo_em.c        |   13 +
 src/scantwo_em.h        |   13 +
 src/scantwo_hk.c        |   13 +
 src/scantwo_hk.h        |   13 +
 src/scantwo_imp.c       |   13 +
 src/scantwo_imp.h       |   13 +
 src/scantwo_mr.c        |   13 +
 src/scantwo_mr.h        |   13 +
 src/simulate.c          |   13 +
 src/simulate.h          |   13 +
 src/simulate_cc.c       |   13 +
 src/simulate_cc.h       |   13 +
 src/stahl_mf.c          |   13 +
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 src/summary_scantwo.c   |   13 +
 src/summary_scantwo.h   |   13 +
 src/util.c              |   13 +
 src/util.h              |   13 +
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 tests/test_io.R         |   14 +
 tests/test_io.Rout.save |   14 +
 139 files changed, 1983 insertions(+), 608 deletions(-)

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Package bnlearn updated to version 1.3 with previous version 1.2 dated 2009-02-05

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 ad advanced plots) are also included.

Diff between bnlearn versions 1.2 dated 2009-02-05 and 1.3 dated 2009-03-29

 Changelog                    |   10 +
 DESCRIPTION                  |   35 +++---
 NAMESPACE                    |    3 
 R/arc.operations.R           |    2 
 R/arc.strength.R             |   76 +++++++++++++
 R/backend-indep.R            |  125 +++-------------------
 R/fast-iamb.R                |   24 ++--
 R/frontend-amat.R            |    2 
 R/frontend-learning.R        |    4 
 R/frontend-plot.R            |   25 ++++
 R/frontend-score.R           |   14 +-
 R/frontend-simulation.R      |    6 -
 R/globals.R                  |   11 +
 R/graph-generation.R         |  238 +++++--------------------------------------
 R/graphviz.R                 |   24 ++--
 R/grow-shrink.R              |   24 ++--
 R/hill-climbing.R            |    6 -
 R/incremental-association.R  |   24 ++--
 R/inter-iamb.R               |   24 ++--
 R/learning-algorithms.R      |   28 ++---
 R/maxmin-pc.R                |   38 +++---
 R/simulation.R               |   14 +-
 R/test.R                     |  225 +++++++++++++++++++++++++++++++---------
 R/utils-amat.R               |   16 --
 R/utils-graph.R              |    2 
 R/utils-misc.R               |   20 ---
 R/utils-sanitization.R       |   46 +++++++-
 R/utils-tests.R              |   11 -
 man/00.bnlearn-package.Rd    |   62 +++++++----
 man/10.gs.Rd                 |   22 +--
 man/11.iamb.Rd               |   18 +--
 man/12.fast.iamb.Rd          |   18 +--
 man/13.inter.iamb.Rd         |   18 +--
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 man/15.hc.Rd                 |   10 -
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 man/22.modelstring.Rd        |   48 ++++----
 man/24.graphgen.Rd           |   53 ++++-----
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 man/31.ci.test.Rd            |   15 --
 man/32.choose.direction.Rd   |    3 
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 man/51.graphviz.plot.Rd      |   19 +--
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 src/allocations.c            |only
 src/bayesian.network.c       |    4 
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 src/common.c                 |   20 +++
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 src/configurations.c         |    6 -
 src/discrete.loglikelihood.c |   28 +----
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 src/is.dag.c                 |  120 +++------------------
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 src/mutual.information.c     |   69 ++----------
 src/path.c                   |   62 +++++------
 src/pearson.x2.c             |   67 ++----------
 66 files changed, 914 insertions(+), 1099 deletions(-)

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Package R2WinBUGS updated to version 2.1-13 with previous version 2.1-12 dated 2009-02-13

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 2.1-12 dated 2009-02-13 and 2.1-13 dated 2009-03-29

 DESCRIPTION            |   49 ++++++++++++++++++++++++++-----------------------
 R/as.mcmc.list.bugs.R  |   15 +++++++--------
 R/bugs.R               |    2 +-
 inst/NEWS              |    6 ++++++
 inst/doc/R2WinBUGS.pdf |    6 +++---
 man/bugs.Rd            |    4 ++--
 6 files changed, 45 insertions(+), 37 deletions(-)

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Permanent link

Package R2HTML updated to version 1.59-1 with previous version 1.59 dated 2008-05-25

Author: Eric Lecoutre
Title: HTML exportation for R objects
Description: Includes HTML function and methods to write in an HTML file. Thus, making HTML reports is easy. Includes a function that allows redirection on the fly, which appears to be very usefull for teaching purpose, as the student can keep a copy of the produced output to keep all that he did during the course. Package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for Sweave allows to parse HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).

Diff between R2HTML versions 1.59 dated 2008-05-25 and 1.59-1 dated 2009-03-29

 DESCRIPTION            |   30 +
 R/HTMLcore.R           |  922 ++++++++++++++++++++++++-------------------------
 man/HTML.data.frame.Rd |  172 ++++-----
 man/HTMLStart.Rd       |  161 ++++----
 4 files changed, 650 insertions(+), 635 deletions(-)

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Package DAAGxtras updated to version 0.7-5 with previous version 0.7-4 dated 2009-01-12

Author: John Maindonald
Title: Data Sets and Functions, supplementary to DAAG
Description: various data sets used in additonal exercises for the book Maindonald, J.H. and Braun, W.J. (2nd edn 2007) "Data Analysis and Graphics Using R", and for a 'Data Mining' course. Note especially the datasets \code{nassCDS} (airbag and other influences on US vehicle accident outcomes: 1997-2002), \code{cricketers} (handedness, British first class cricketers born before 1961 whose handedness was specified), \code{nswdemo} and related datasets (US Labor Training Evaluation Data), \code{rockArt} (multivariate binary data on Pacific rock art), \code{hotspots} (ages and distance from Kilauea of larval hotspots; c.f. also \code{hotspots2006}), \code{nihills} (record times for Northern Ireland mountain races), \code{worldRecords} (record times for track and road races), \code{progression} (progression of record times for track races), \code{edcT} and \code{edcCO2} (temperature and CO2 estimates from the EPICA Dome C ice core, covering 0 to 800 kyr BP), \code{grog} (Australian and NZ liquor consumption patterns, 1998-2006), and \code{bomregions} (historical Australian climate data).

Diff between DAAGxtras versions 0.7-4 dated 2009-01-12 and 0.7-5 dated 2009-03-29

 DESCRIPTION           |   44 ++++++++++++++++++++++++--------------------
 data/SOI.RData        |binary
 data/cricketers.RData |only
 man/SOI.Rd            |    4 ++--
 man/cricketers.Rd     |only
 5 files changed, 26 insertions(+), 22 deletions(-)

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Permanent link

Sat, 28 Mar 2009

New package polydect with initial version 0.1-2
Package: polydect
Version: 0.1-2
Date: 2008-04-21
Title: polydect
Author: Zhihua Su
Maintainer: Zhihua Su
Depends: R (>= 2.4.1)
Description: functions for one-dimension jump position detection using one-sided polynomial kernel detectors (polynomial order from 0 to 3)
License: X11
Packaged: Fri Mar 27 17:04:29 2009; suzhihua
Repository: CRAN
Date/Publication: 2009-03-28 11:58:22

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Package ipred updated to version 0.8-7 with previous version 0.8-6 dated 2008-08-07

Author: Andrea Peters and Torsten Hothorn
Title: Improved Predictors
Description: Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

Diff between ipred versions 0.8-6 dated 2008-08-07 and 0.8-7 dated 2009-03-28

 CHANGES                         |    6 +
 DESCRIPTION                     |   14 +--
 R/predict.bagging.R             |    4 
 R/sbrier.R                      |    4 
 inst/doc/ipred-examples.pdf     |binary
 man/DLBCL.Rd                    |    2 
 man/GBSG2.Rd                    |    2 
 man/sbrier.Rd                   |    8 -
 tests/ipred-bugs.Rout.save      |   11 +-
 tests/ipred-segfault.R          |    2 
 tests/ipred-segfault.Rout.save  |  179 ++++++++++++++++------------------------
 tests/ipred-smalltest.Rout.save |only
 tests/ipred-tests.R             |   12 +-
 tests/ipred-tests.Rout.save     |   23 ++---
 14 files changed, 122 insertions(+), 145 deletions(-)

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New package alphahull with initial version 0.1
Package: alphahull
Title: Generalization of the convex hull of a sample of points in the plane
Version: 0.1
Date: 2009-03-26
Author: Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal.
Maintainer: Beatriz Pateiro-Lopez
Depends: tripack
Description: This package computes the alpha-shape and alpha-convex hull of a given sample of points in the plane. The concepts of alpha-shape and alpha-convex hull generalize the definition of the convex hull of a finite set of points. The programming is based on the duality between the Voronoi diagram and Delaunay triangulation. The package also includes a function that returns the Delaunay mesh of a given sample of points and its dual Voronoi diagram in one single object.
License: file LICENSE
Packaged: Sat Mar 28 12:14:23 2009; beatriz
Repository: CRAN
Date/Publication: 2009-03-28 11:58:18

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Package QCA updated to version 0.5-3 with previous version 0.5-2 dated 2009-02-09

Author: Adrian Dusa
Title: Qualitative Comparative Analysis
Description: Performs the Quine-McCluskey algorithm for Qualitative Comparative Analysis, as described in Ragin, Charles C. 1987 "The Comparative Method. Moving beyond qualitative and quantitative strategies", Berkeley: University of California Press. In the classical approach it currently handles about 15 conditions and one outcome, but since version 0.4-5 the package has an enhanced, faster function that obtains the same exact solutions with a substantially lower memory consumption, and it handles even more causal conditions. The next versions of this algorithm will be oriented towards multi-value and fuzzy-set functions. Also, in the near future the current functions will deal with missing values in the data

Diff between QCA versions 0.5-2 dated 2009-02-09 and 0.5-3 dated 2009-03-28

 DESCRIPTION        |   21 +++++++++++++++++----
 R/truthTable.R     |   18 ++++++++++--------
 R/verifyQCA.R      |    8 --------
 inst/CHANGES       |   13 ++++++++++---
 man/QCA.package.Rd |    4 ++--
 5 files changed, 39 insertions(+), 25 deletions(-)

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Package ChainLadder updated to version 0.1.2-11 with previous version 0.1.2-10 dated 2009-03-27

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

Diff between ChainLadder versions 0.1.2-10 dated 2009-03-27 and 0.1.2-11 dated 2009-03-28

 DESCRIPTION                  |    8 ++++----
 NEWS                         |   10 ++++++++--
 R/MackChainLadderFunctions.R |   11 +++++++----
 man/MackChainLadder.Rd       |    2 +-
 4 files changed, 20 insertions(+), 11 deletions(-)

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New package ModelMap with initial version 1.1.11
Package: ModelMap
Type: Package
Title: Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps.
Version: 1.1.11
Date: 2009-03-27
Depends: R (>= 2.8.1), randomForest, gbm, PresenceAbsence, rgdal
Author: Elizabeth Freeman, Tracey Frescino
Maintainer: Elizabeth Freeman
Description: This package will create sophisticated models of training data and validate the models with an independant test set, cross validation, or in the case of Random Forest Models, with Out OF Bag (OOB) predictions on the training data. It will creat graphs and tables of the model validation results. It will apply these models to GIS .img files of predictors to create detailed prediction surfaces. It will handle large predictor files for map making, by reading in the .img files in chuncks, and output to the .txt file the prediction for each data chunk, before reading the next chenk of data.
License: Unlimited
Packaged: Fri Mar 27 14:07:49 2009; eafreeman
Repository: CRAN
Date/Publication: 2009-03-28 10:20:34

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Package Animal updated to version 1.01 with previous version 1.0 dated 2009-03-18

Author: Matti Pastell
Title: Analyze time-coded animal behavior data
Description: The Animal package is a collection of functions for analyzing animal (including humans) behavior data originating from a variety of sources. The package has functions to analyze time coded behaviors from CowLog (open source software for coding behaviors from digital video) data files and observation files with similar format. Other features include hourly, daily, weekly and monthly summaries of time coded data, analysis of RIC (roughage intake system, Insentec automation) data files and labeling measurement data according to behavioral observations for e.g model building purpose.

Diff between Animal versions 1.0 dated 2009-03-18 and 1.01 dated 2009-03-28

 DESCRIPTION       |   26 ++++++++++++++++----------
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Fri, 27 Mar 2009

Package qpcR updated to version 1.1-8 with previous version 1.1-7 dated 2008-12-16

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 1.1-7 dated 2008-12-16 and 1.1-8 dated 2009-03-27

 qpcR-1.1-7/qpcR/man/qpcR.Rd           |only
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 qpcR-1.1-8/qpcR/R/expcomp.R           |    2 +-
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 qpcR-1.1-8/qpcR/R/modlist.R           |    2 +-
 qpcR-1.1-8/qpcR/R/pcrbatch.R          |    2 +-
 qpcR-1.1-8/qpcR/R/pcrfit.R            |    2 +-
 qpcR-1.1-8/qpcR/R/pcropt1.R           |    2 +-
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New package primer with initial version 0.1
Package: primer
Type: Package
Title: Functions and data for the forthcoming, A Primer of Ecology with R
Version: 0.1
Date: 2008-09-19
Author: M Henry H Stevens
Maintainer: Hank Stevens
Depends: deSolve, lattice
Suggests: bbmle, gdata, nlme, vegan
Description: Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.
License: GPL
LazyLoad: yes
Packaged: Fri Mar 27 07:51:08 2009; stevenmh
Repository: CRAN
Date/Publication: 2009-03-27 16:40:00

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Package party updated to version 0.9-996 with previous version 0.9-995 dated 2009-02-23

Author: Torsten Hothorn, Kurt Hornik, Carolin Strobl and Achim Zeileis
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.

Diff between party versions 0.9-995 dated 2009-02-23 and 0.9-996 dated 2009-03-27

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Package mboost updated to version 1.1-0 with previous version 1.0-6 dated 2009-01-09

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 1.0-6 dated 2009-01-09 and 1.1-0 dated 2009-03-27

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Package HardyWeinberg updated to version 1.3 with previous version 1.2 dated 2008-04-22

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 1.2 dated 2008-04-22 and 1.3 dated 2009-03-27

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Package seewave updated to version 1.5.4 with previous version 1.5.2 dated 2009-01-03

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.

Diff between seewave versions 1.5.2 dated 2009-01-03 and 1.5.4 dated 2009-03-27

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Package rbenchmark updated to version 0.2 with previous version 0.1 dated 2009-03-20

Author: Wacek Kusnierczyk
Title: Benchmarking routine for R
Description: rbenchmark is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.

Diff between rbenchmark versions 0.1 dated 2009-03-20 and 0.2 dated 2009-03-27

 DESCRIPTION              |    8 ++++----
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New package bethel with initial version 0.1
Package: bethel
Version: 0.1
Date: 2009-03-22
Author: Michele De Meo
Maintainer: Michele De Meo
Title: Bethel's algorithm.
Description: The sample size according to the Bethel's procedure.
Depends: R (>= 2.5.0)
License: GPL (>= 2)
Packaged: Fri Mar 27 10:54:06 2009; Administrator
Repository: CRAN
Date/Publication: 2009-03-27 10:52:49

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New package arulesNBMiner with initial version 0.1-0
Package: arulesNBMiner
Version: 0.1-0
Date: 2008-03-26
Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Author: Michael Hahsler
Maintainer: Michael Hahsler
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets presented in "Michael Hahsler. A model-based frequency constraint for mining associations from transaction data. Data Mining and Knowledge Discovery, 13(2):137-166, September 2006." In addition an extension for NB-precise rules is implemented.
Depends: arules (>= 0.6-6), rJava (>= 0.6-0)
Imports: methods
License: GPL-2
Copyright: All code is Copyright (C) Michael Hahsler
Packaged: Thu Mar 26 20:34:44 2009; hahsler
Repository: CRAN
Date/Publication: 2009-03-27 10:44:18

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New package tiger with initial version 0.1
Package: tiger
Type: Package
Title: TIme series of Grouped ERrors
Version: 0.1
Date: 2009-02-26
Author: Dominik Reusser
Maintainer: Dominik Reusser
Description: Temporally resolved groups of typical differences (errors) between two time series are determined and visualized
Depends: R (>= 1.8.0), e1071, hexbin, qualV
License: GPL-2
Packaged: Thu Mar 26 18:56:03 2009; dreusser
Repository: CRAN
Date/Publication: 2009-03-27 08:11:33

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Package survey updated to version 3.13 with previous version 3.12 dated 2009-03-22

Author: Thomas Lumley
Title: analysis of complex survey samples
Description: Summary statistics, generalised linear models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase designs. Graphics.

Diff between survey versions 3.12 dated 2009-03-22 and 3.13 dated 2009-03-27

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Package stashR updated to version 0.3-3 with previous version 0.3-2 dated 2008-05-02

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

Diff between stashR versions 0.3-2 dated 2008-05-02 and 0.3-3 dated 2009-03-27

 DESCRIPTION           |   29 +++++++++++++++--------------
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Package psych updated to version 1.0-67 with previous version 1.0-65 dated 2009-02-08

Author: William Revelle
Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. For more information, see the personality-project.org/r webpage.

Diff between psych versions 1.0-65 dated 2009-02-08 and 1.0-67 dated 2009-03-27

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New package mvgraph with initial version 1.0
Package: mvgraph
Version: 1.0
Type: Package
Title: Multivariate, Interactive Visualization
Date: 2008-11-17
Author: Moritz Gschwandtner
Maintainer: Moritz Gschwandtner
Depends: StatDA
Description: This package offers different possibilities to visualize multivariate data
License: GPL (>= 3)
Packaged: Thu Mar 26 16:47:29 2009; moritz
Repository: CRAN
Date/Publication: 2009-03-27 08:10:46

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New package fast with initial version 0.51
Package: fast
Type: Package
Title: Implementation of the Fourier Amplitute Sensitivity Test (FAST)
Version: 0.51
Date: 2008-11-26
Author: Dominik Reusser
Maintainer: Dominik Reusser
Description: The Fourier Amplitute Sensitivity Test (FAST) is a method to deterimine global sensitivities of a model on parameter changes with relavtively few model runs. This package implements this sensitivity analysis method.
License: GPL-2
Packaged: Thu Mar 26 18:57:23 2009; dreusser
Repository: CRAN
Date/Publication: 2009-03-27 08:10:42

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Package caret updated to version 4.10 with previous version 4.08 dated 2009-02-19

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

Diff between caret versions 4.08 dated 2009-02-19 and 4.10 dated 2009-03-27

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Package ChainLadder updated to version 0.1.2-10 with previous version 0.1.2-9 dated 2009-02-01

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

Diff between ChainLadder versions 0.1.2-9 dated 2009-02-01 and 0.1.2-10 dated 2009-03-27

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Thu, 26 Mar 2009

Package mgcv updated to version 1.5-2 with previous version 1.5-1 dated 2009-03-17

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 changeLOS updated to version 2.0.9-2 with previous version 2.0.9-1 dated 2009-02-01

Author: Matthias Wangler , Jan Beyersmann
Title: Change in LOS
Description: Change in length of hospital stay (LOS) is frequently used to assess the impact and the costs of hospital-acquired complications. In order to compute the attributable change in LOS, it is crucial to account for the timing of events: A complication can only have an effect on LOS, once it has occured. These temporal dynamics can be adequately handled by multistate models; however, there is few software for such models available. We introduce an R-package "changeLOS" for computing change in LOS based on methods described in Schulgen and Schumacher (1996). We will illustrate the program on data from a prospective cohort study on hospital-acquired infections. Main features of the R-package "changeLOS" are R-methods to: (1) describe the multi-state model. (2) compute the Aalen-Johansen estimator for the matrix of transition probabilities P(u-, u) for all observed transition times u.(3) compute the Aalen-Johansen estimator for the matrix of transition probabilities P(s,t); the estimator is a finite matrix product of matrices P(u-,u) for every observed event time in the interval(s,t]. (4) visualize the temporal dynamics of the data, illustrated by transition probabilities. (5) compute and visualize change in LOS. (6) compute bootstrap variances for change in LOS.

Diff between changeLOS versions 2.0.9-1 dated 2009-02-01 and 2.0.9-2 dated 2009-03-26

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 2 files changed, 29 insertions(+), 5 deletions(-)

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Package nsRFA updated to version 0.6-7 with previous version 0.6-6 dated 2009-01-14

Author: Alberto Viglione
Title: Non-supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves.

Diff between nsRFA versions 0.6-6 dated 2009-01-14 and 0.6-7 dated 2009-03-26

 DESCRIPTION     |   23 +++++++++++++----------
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 man/HOMTESTS.Rd |   12 +++++++++---
 3 files changed, 37 insertions(+), 17 deletions(-)

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Package homtest updated to version 1.0-4 with previous version 1.0-2 dated 2007-10-03

Author: Alberto Viglione
Title: Homogeneity tests for Regional Frequency Analysis
Description: A collection of homogeneity tests described in: Viglione A., Laio F., Claps P. (2007) ``A comparison of homogeneity tests for regional frequency analysis'', Water Resources Research, 43, W03428, doi:10.1029/2006WR005095. More on Regional Frequency Analysis can be found in package nsRFA.

Diff between homtest versions 1.0-2 dated 2007-10-03 and 1.0-4 dated 2009-03-26

 DESCRIPTION  |   19 ++++++++++++-------
 R/HOMTESTS.R |    6 ++++--
 2 files changed, 16 insertions(+), 9 deletions(-)

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New package isotone with initial version 0.8-1
Package: isotone
Type: Package
Title: Active set and generalized PAVA for isotone optimization
Version: 0.8-1
Date: 2009-03-24
Author: Jan de Leeuw, Kurt Hornik, Patrick Mair
Maintainer: Jan de Leeuw
Description: This package contains two main functions: gpava() for solving general isotone regression problem using the pool-adjacent-violators algorithm (PAVA). activeSet() provides a framwork of active set methods for isotone optimization problems. Various loss functions are pre-spcified.
License: GPL
URL: http://r-forge.r-project.org/projects/psychor/
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: psychor
Repository/R-Forge/Revision: 86
Publication/Date: 2009-03-24 09:33:15
Packaged: Wed Mar 25 05:17:32 2009; rforge
Date/Publication: 2009-03-26 09:46:51

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Package clim.pact updated to version 2.2-31 with previous version 2.2-30 dated 2009-03-04

Author: Rasmus E. Benestad
Title: Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.
Description: The package contains R functions for retrieving data, making climate analysis and downscaling of monthly mean and daily mean global climate scenarios. (Windows-users may need to obtain the 'ncdf' package from URL 'http://www.stats.ox.ac.uk/pub/RWin/' to get clim.pact to work). The package is also described in the book 'Empirical-Statistical Downscaling (http://www.worldscibooks.com/environsci/6908.html)

Diff between clim.pact versions 2.2-30 dated 2009-03-04 and 2.2-31 dated 2009-03-26

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Package cairoDevice updated to version 2.10 with previous version 2.9-2 dated 2008-10-07

Author: Michael Lawrence
Title: Cairo-based cross-platform antialiased graphics device driver.
Description: Cairo/GTK graphics device driver with output to screen, file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or Cairo context). The screen device may be embedded into RGtk2 interfaces. Supports all interactive features of other graphics devices, including getGraphicsEvent().

Diff between cairoDevice versions 2.9-2 dated 2008-10-07 and 2.10 dated 2009-03-26

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Package RGtk2 updated to version 2.12.10 with previous version 2.12.9 dated 2009-02-20

Author: Michael Lawrence and Duncan Temple Lang
Title: R bindings for Gtk 2.8.0 and above
Description: Facilities in the R language for programming graphical interfaces using Gtk, the Gimp Tool Kit.

Diff between RGtk2 versions 2.12.9 dated 2009-02-20 and 2.12.10 dated 2009-03-26

 DESCRIPTION        |   18 +++++++++++-------
 src/Makevars       |    2 +-
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New package WriteXLS with initial version 1.5.0
Package: WriteXLS
Version: 1.5.0
Date: 2009-03-24
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.
Author: Marc Schwartz
Maintainer: Marc Schwartz
License: GPL (>=2)
SystemRequirements: Perl, OLE::Storage_Lite, Parse::RecDescent, Getopt::Long, File::Basename, Spreadsheet::WriteExcel, Encode, File::Glob, Text::CSV_XS
Repository: CRAN
Repository/R-Forge/Project: writexls
Repository/R-Forge/Revision: 14
Publication/Date: 2009-03-24 22:17:19
Packaged: Wed Mar 25 05:06:49 2009; rforge
Date/Publication: 2009-03-26 08:42:36

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New package BMN with initial version 1.0
Package: BMN
Type: Package
Title: The pseudo-likelihood method for pairwise binary markov networks
Version: 1.0
Date: 2009-03-19
Author: Holger Hoefling
Maintainer: Holger Hoefling
Description: This package implements approximate and exact methods for pairwise binary markov models. The exact method uses an implementation of the junction tree algorithm for binary graphical models. For more details see the help files
License: GPL-2
Depends: R (>= 2.6.0)
Packaged: Wed Mar 25 14:53:15 2009; hhoeflin
Repository: CRAN
Date/Publication: 2009-03-26 08:29:24

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Wed, 25 Mar 2009

Package bcp updated to version 2.1.1 with previous version 2.1 dated 2008-07-16

Author: Chandra Erdman and John W. Emerson
Title: A Package for Performing a Bayesian Analysis of Change Point Problems
Description: An implementation of the Barry and Hartigan (1993) product partition model for the standard change point problem using Markov Chain Monte Carlo.

Diff between bcp versions 2.1 dated 2008-07-16 and 2.1.1 dated 2009-03-25

 DESCRIPTION          |   15 ++++++++++-----
 man/interval.prob.Rd |    2 +-
 src/Cbcp.cpp         |    4 ++--
 3 files changed, 13 insertions(+), 8 deletions(-)

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New package lcda with initial version 0.1
Package: lcda
Type: Package
Title: Latent Class Discriminant Analysis
Version: 0.1
Date: 2009-03-25
Depends: R (>= 2.6.0), poLCA
Author: Michael Buecker
Maintainer: Michael Buecker
Description: Local Discrimination via Latent Class Models
License: GPL
Packaged: Wed Mar 25 11:41:45 2009; michael
Repository: CRAN
Date/Publication: 2009-03-25 17:49:23

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Package TSpadi updated to version 2009.3-2 with previous version 2009.3-1 dated 2009-03-22

Author: Paul Gilbert
Title: Time Series Database Interface extensions for PADI Time Series Server
Description: Provides methods for generics in the TSdbi package to connect through a protocol for application database interface (PADI) to a time series database (e.g. Fame).

Diff between TSpadi versions 2009.3-1 dated 2009-03-22 and 2009.3-2 dated 2009-03-25

 DESCRIPTION             |   14 ++++++++------
 inst/doc/TSpadiFame.pdf |binary
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Package TSodbc updated to version 2009.3-2 with previous version 2009.3-1 dated 2009-03-22

Author: Paul Gilbert
Title: Time Series Database Interface extensions for ODBC
Description: TSodbc provides a ODBC interface for TSdbi.

Diff between TSodbc versions 2009.3-1 dated 2009-03-22 and 2009.3-2 dated 2009-03-25

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Package TSPostgreSQL updated to version 2009.3-2 with previous version 2009.3-1 dated 2009-03-22

Author: Paul Gilbert
Title: Time Series Database Interface extensions for PostgreSQL
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi.

Diff between TSPostgreSQL versions 2009.3-1 dated 2009-03-22 and 2009.3-2 dated 2009-03-25

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Package TSMySQL updated to version 2009.3-2 with previous version 2009.3-1 dated 2009-03-22

Author: Paul Gilbert
Title: Time Series Database Interface extensions for MySQL
Description: TSMySQL provides a MySQL interface for TSdbi.

Diff between TSMySQL versions 2009.3-1 dated 2009-03-22 and 2009.3-2 dated 2009-03-25

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Package SimComp updated to version 1.3 with previous version 1.2 dated 2008-11-25

Author: Mario Hasler
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals for general linear hypotheses when there is more than one primary response variable (endpoint). The procedure of Hasler (2009) is applied for differences or ratios of means of normally distributed data. The covariance matrices (containing the covariances between the endpoints) may be assumed to be equal or possibly unequal for the different groups.

Diff between SimComp versions 1.2 dated 2008-11-25 and 1.3 dated 2009-03-25

 DESCRIPTION            |   39 ++++++++++++++++++++-------------------
 R/SimTestDiffHet.R     |    3 ++-
 R/SimTestDiffHom.R     |    3 ++-
 R/SimTestRatHet.R      |    3 ++-
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 man/SimCiDiff.Rd       |    9 ++++++---
 man/SimCiRat.Rd        |    9 ++++++---
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Package relax updated to version 1.2.1 with previous version 1.1 dated 2008-12-01

Author: Hans Peter Wolf
Title: relax -- R Editor for Literate Analysis and lateX
Description: package relax contains some functions for report writing, presentation, and programming: relax(), tangleR(), weaveR(), slider(). "relax" is written in R and Tcl/Tk. relax creates a new window (top level Tcl/Tk widget) that consists of two text fields and some buttons and menus. Text (chunks) and code (chunks) are inserted in the upper text field (report field). Code chunks are evaluated by clicking on EvalRCode. Results are shown in the lower text field (output field) and will be transfered to the report field by pressing on Insert. In this way you get correct reports. These reports can be loaded again in cause of presentation, modification and result checking. tangleR() and weaveR() implement a plain kind of tangling and weaving. slider() is designed to define sliders for interactive experiments in a simple way. The syntax rules of code chunks and text chunks are defined by the noweb system proposed by Norman Ramsey (http://www.eecs.harvard.edu/~nr/noweb/intro.html). For integrating jpeg graphics into the text field you need the Tcl/Tk Img package of Jan Nijtmans (see: http://members.chello.nl/~j.nijtmans/img.html, http://home.kpnplanet.nl/~J.Nijtmans@kpnplanet.nl/img.html or http://tkimg.sourceforge.net/, the package is found on http://sourceforge.net/projects/tkimg). If an Img version is integrated in the relax package the license terms concerning the img package will be found in the source file of the package, for example in: relax/src/tkimg1.3.tar.gz. Older windows versions of relax contain the Tcl/Tk img package, so no further installations have to be done.

Diff between relax versions 1.1 dated 2008-12-01 and 1.2.1 dated 2009-03-25

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 R/slider.R                 |    3 
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Package nlrwr updated to version 1.0-6 with previous version 1.0-5 dated 2009-01-07

Author: Christian Ritz ,
Title: Nonlinear regression with R
Description: Datasets and functions for nonlinear regression. Support software for the book "Nonlinear regression with R".

Diff between nlrwr versions 1.0-5 dated 2009-01-07 and 1.0-6 dated 2009-03-25

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Package ncf updated to version 1.1-3 with previous version 1.1-2 dated 2009-02-18

Author: Ottar N. Bjornstad
Title: spatial nonparametric covariance functions
Description: R functions for analyzing spatial (cross-)covariance: the nonparametric (cross-)covariance, the spline correlogram, the nonparametric phase coherence function, and related.

Diff between ncf versions 1.1-2 dated 2009-02-18 and 1.1-3 dated 2009-03-25

 DESCRIPTION |    8 +++++---
 R/ncf.R     |    4 ++--
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 3 files changed, 9 insertions(+), 5 deletions(-)

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Package drc updated to version 1.6-1 with previous version 1.6-0 dated 2009-03-24

Author: Christian Ritz , Jens Strebig
Title: Analysis of dose-response curves
Description: Analysis of one or multiple curves with focus on concentration-response, dose-response and time-response curves used, for example in biology, environmental sciences, medicine, pharmacology, toxicology.

Diff between drc versions 1.6-0 dated 2009-03-24 and 1.6-1 dated 2009-03-25

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Package Rlabkey updated to version 0.0.6 with previous version 0.0.5 dated 2009-01-12

Author: Valerie Obenchain
Title: Data retrieval from a Labkey database
Description: This package imports data from a labkey database into an R data frame

Diff between Rlabkey versions 0.0.5 dated 2009-01-12 and 0.0.6 dated 2009-03-25

 DESCRIPTION              |   14 +++++++++-----
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Package ISOcodes updated to version 0.2-3 with previous version 0.2-1 dated 2009-03-17

Author: Christian Buchta and Kurt Hornik
Title: Selected ISO codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 and ISO 10646 character codes as well as the Unicode data table.

Diff between ISOcodes versions 0.2-1 dated 2009-03-17 and 0.2-3 dated 2009-03-25

 DESCRIPTION        |    8 ++++----
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Tue, 24 Mar 2009

Package spBayes updated to version 0.1-2 with previous version 0.1-1 dated 2009-03-03

Author: Andrew O. Finley , Sudipto Banerjee , Bradley P. Carlin
Title: Univariate and Multivariate Spatial Modeling
Description: spBayes fits univariate and multivariate models with Markov chain Monte Carlo (MCMC).

Diff between spBayes versions 0.1-1 dated 2009-03-03 and 0.1-2 dated 2009-03-24

 DESCRIPTION                   |   15 ++++++++++-----
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Package seriation updated to version 1.0-0 with previous version 0.1-6 dated 2008-09-29

Author: Michael Hahsler, Christian Buchta and Kurt Hornik
Title: Infrastructure for seriation
Description: Infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also contains some visualizations techniques based on seriation.

Diff between seriation versions 0.1-6 dated 2008-09-29 and 1.0-0 dated 2009-03-24

 DESCRIPTION            |   29 +++++++++++++++++------------
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New package sisus with initial version 0.09-011
Package: sisus
Type: Package
Title: SISUS: Stable Isotope Sourcing using Sampling
Version: 0.09-011
Date: 2008-05-22
Author: Erik Barry Erhardt
Maintainer: Erik Barry Erhardt
Description: SISUS for source partitioning using stable isotopes.
Depends: R (>= 2.7.0), annotate, ash, Biobase, coda, ellipse, gclus, gdata, geneplotter, gplots, gtools, hdrcde, moments, mvtnorm, polyapost, rcdd, RColorBrewer, stats, sm
License: GPL-3
Packaged: Tue Mar 24 08:05:41 2009; erike
Repository: CRAN
Date/Publication: 2009-03-24 18:56:46

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Package bipartite updated to version 0.90 with previous version 0.85 dated 2009-03-11

Author: Carsten F. Dormann and Bernd Gruber, with additional code from Jochen Fruend, 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 0.85 dated 2009-03-11 and 0.90 dated 2009-03-24

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Package arules updated to version 1.0-0 with previous version 0.6-8 dated 2009-01-16

Author: Michael Hahsler, Christian Buchta, Bettina Gruen and Kurt Hornik
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides interfaces to C implementations of the association mining algorithms Apriori and Eclat by C. Borgelt.

Diff between arules versions 0.6-8 dated 2009-01-16 and 1.0-0 dated 2009-03-24

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Package ars updated to version 0.4 with previous version 0.3 dated 2009-01-26

Author: Paulino Perez Rodriguez original C++ code from Arnost Komarek based on ars.f written by P. Wild and W. R. Gilks
Title: Adaptive Rejection Sampling
Description: Adaptive Rejection Sampling, Original version

Diff between ars versions 0.3 dated 2009-01-26 and 0.4 dated 2009-03-24

 DESCRIPTION |   24 ++++++++++++++----------
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Package TSP updated to version 1.0-0 with previous version 0.2-6 dated 2009-02-07

Author: Michael Hahsler and Kurt Hornik
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling salesperson problem (TSP). The package provides some simple algorithms and an interface to Concorde, the currently fastest TSP solver. Concorde itself is not included in the package and has to be obtained separately.

Diff between TSP versions 0.2-6 dated 2009-02-07 and 1.0-0 dated 2009-03-24

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Package FrF2 updated to version 0.9-1 with previous version 0.9 dated 2009-03-11

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; structures and even function names may change in the future.

Diff between FrF2 versions 0.9 dated 2009-03-11 and 0.9-1 dated 2009-03-24

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Package spgwr updated to version 0.5-7 with previous version 0.5-5 dated 2009-01-14

Author: Roger Bivand and Danlin Yu
Title: Geographically weighted regression
Description: Functions for computing geographically weighted regressions based on work by Chris Brunsdon, Martin Charlton and Stewart Fortheringham, http://ncg.nuim.ie/ncg/GWR/index.htm

Diff between spgwr versions 0.5-5 dated 2009-01-14 and 0.5-7 dated 2009-03-24

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Package xtable updated to version 1.5-5 with previous version 1.5-4 dated 2008-10-05

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

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Package s20x updated to version 3.1-5 with previous version 3.1-4 dated 2009-02-23

Author: Andrew Balemi, James Curran, Brant Deppa, Mike Forster, Charlotte Maia, Chris Wild
Title: Stats 20x
Description: Stats 20x functions.

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Package rattle updated to version 2.4.54 with previous version 2.4.47 dated 2009-03-16

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 2.4.47 dated 2009-03-16 and 2.4.54 dated 2009-03-24

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New package dyad with initial version 1.0
Package: dyad
Title: Analysis of dyadic observational data
Version: 1.0
Date: 2008-12-23
Author: Tara Madhyastha , Ellen Hamaker
Maintainer: Tara Madhyastha
Depends: R (>= 2.6.2)
Description: Contains original implementation of the Gottman-Murray marriage model and revisions using threshold autoregressive models. These programs allow modeling of dyadic observational data, such as interaction between husband and wife. Intended for researchers interested in modeling social behavior.
License: GPL-2
Packaged: Mon Mar 23 13:29:58 2009; Tmadhyastha
Repository: CRAN
Date/Publication: 2009-03-24 07:58:37

More information about dyad at CRAN
Permanent link

Package drc updated to version 1.6-0 with previous version 1.5-5 dated 2009-02-08

Author: Christian Ritz , Jens Strebig
Title: Analysis of dose-response curves
Description: Analysis of one or multiple curves with focus on concentration-response, dose-response and time-response curves used, for example in biology, environmental sciences, medicine, pharmacology, toxicology.

Diff between drc versions 1.5-5 dated 2009-02-08 and 1.6-0 dated 2009-03-24

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Package dplR updated to version 1.1.8 with previous version 1.1.7 dated 2009-03-13

Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some standard tree-ring analyses.

Diff between dplR versions 1.1.7 dated 2009-03-13 and 1.1.8 dated 2009-03-24

 DESCRIPTION   |    8 ++++----
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Package aster updated to version 0.7-7 with previous version 0.7-6 dated 2009-01-12

Author: Charles J. Geyer .
Title: Aster Models
Description: functions and datasets for Aster modeling (forest graph exponential family conditional or unconditional canonical statistic models for life history analysis)

Diff between aster versions 0.7-6 dated 2009-01-12 and 0.7-7 dated 2009-03-24

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Mon, 23 Mar 2009

Package spcosa updated to version 0.1-2 with previous version 0.1-1 dated 2009-03-13

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

Diff between spcosa versions 0.1-1 dated 2009-03-13 and 0.1-2 dated 2009-03-23

 DESCRIPTION                                |    8 
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Package aspect updated to version 0.8-1 with previous version 0.8-0 dated 2009-03-14

Author: Jan de Leeuw, Patrick Mair
Title: Aspects of Multivariables
Description: This package consists of two main functions: The first function is corAspect() performs optimal scaling by maximizing an aspect (i.e. target function such as sum eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. The second function is lineals() which performs optimal scaling by mimimization a non-correlational aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as SEM. A platform including related PsychoR packages is provided on R-forge.

Diff between aspect versions 0.8-0 dated 2009-03-14 and 0.8-1 dated 2009-03-23

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New package LambertW with initial version 0.1.0
Package: LambertW
Type: Package
Title: Lambert W parameter estimation
Version: 0.1.0
Date: 2009-03-21
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
Description: Estimation, plotting, testing of Lambert W random variables
Depends: moments, gsl, MASS, maxLik, nortest
License: GPL-2
LazyLoad: yes
Packaged: Mon Mar 23 18:52:40 2009; hornik
Repository: CRAN
Date/Publication: 2009-03-23 18:07:08

More information about LambertW at CRAN
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Package plotpc updated to version 1.0-2 with previous version 1.0-1 dated 2009-03-10

Author: Stephen Milborrow
Title: Plot principal component histograms around a scatter plot.
Description: Plot principal component histograms around a bivariate scatter plot.

Diff between plotpc versions 1.0-1 dated 2009-03-10 and 1.0-2 dated 2009-03-23

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Package earth updated to version 2.3-2 with previous version 2.3-1 dated 2009-02-26

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 2.3-1 dated 2009-02-26 and 2.3-2 dated 2009-03-23

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New package HadoopStreaming with initial version 0.1
Package: HadoopStreaming
Type: Package
Title: Utilities for using R scripts in Hadoop streaming
Version: 0.1
Date: 2009-03-16
Author: David S. Rosenberg
Maintainer: David S. Rosenberg
Depends: getopt
Description: Provides a framework for writing map/reduce scripts for use in Hadoop Streaming. Also facilitates operating on data in a streaming fashion, without Hadoop.
License: GPL
Packaged: Sat Mar 21 11:42:46 2009; drosen
Repository: CRAN
Date/Publication: 2009-03-23 11:09:20

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Package rtv updated to version 0.2.2 with previous version 0.2.0 dated 2009-03-19

Author: Charlotte Maia
Title: Random Time Variable Objects
Description: An R package for conveniently representing and manipulating realisations of random time variables.

Diff between rtv versions 0.2.0 dated 2009-03-19 and 0.2.2 dated 2009-03-23

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Sun, 22 Mar 2009

Package survey updated to version 3.12 with previous version 3.11-2 dated 2009-02-24

Author: Thomas Lumley
Title: analysis of complex survey samples
Description: Summary statistics, generalised linear models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase designs. Graphics.

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Package sn updated to version 0.4-12 with previous version 0.4-11 dated 2009-01-30

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

Diff between sn versions 0.4-11 dated 2009-01-30 and 0.4-12 dated 2009-03-22

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Package qtlbim updated to version 1.9.3 with previous version 1.9.2 dated 2009-02-28

Author: Brian S. Yandell and Nengjun Yi , with contributions from Tapan Mehta, Samprit Banerjee, Daniel Shriner and Ramprasad Venkataraman (UA-Birmingham), Jee Young Moon, W. Whipple Neely (UW-Madison) and Hao Wu and Randy von Smith (Jackson Laboratory).
Title: QTL Bayesian Interval Mapping
Description: Functions for model selection for genetic architecture.

Diff between qtlbim versions 1.9.2 dated 2009-02-28 and 1.9.3 dated 2009-03-22

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Package nleqslv updated to version 1.3 with previous version 1.1 dated 2009-02-16

Author: Berend Hasselman
Title: Solve systems of non linear equations
Description: Solve a system of non linear equations using a Broyden or a Newton method with a choice of global strategies such as linesearch and trust region. There are options for using a numerical or an analytical jacobian and fixed or automatic scaling of parameters.

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Package muhaz updated to version 1.2.4 with previous version 1.2.3 dated 2006-04-09

Author: S original by Kenneth Hess, R port by R. Gentleman
Title: Hazard Function Estimation in Survival Analysis
Description: A package for producing a smooth estimate of the hazard function for censored data.

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Package TSpadi updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extensions for PADI Time Series Server
Description: Provides methods for generics in the TSdbi package to connect through a protocol for application database interface (PADI) to a time series database (e.g. Fame).

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Package TSodbc updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extensions for ODBC
Description: TSodbc provides a ODBC interface for TSdbi.

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Package TSfame updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extensions for fame
Description: TSfame provides a fame interface for TSdbi.

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Package TSSQLite updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extentions for SQLite
Description: TSSQLite provides a SQLite interface for TSdbi.

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Package TSPostgreSQL updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extensions for PostgreSQL
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi.

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Package TSMySQL updated to version 2009.3-1 with previous version 2008.11-1 dated 2008-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extensions for MySQL
Description: TSMySQL provides a MySQL interface for TSdbi.

Diff between TSMySQL versions 2008.11-1 dated 2008-11-03 and 2009.3-1 dated 2009-03-22

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Sat, 21 Mar 2009

Package mnormt updated to version 1.3-3 with previous version 1.3-2 dated 2009-01-30

Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Title: The multivariate normal and t distributions
Description: This package provides functions for computing the density and the distribution function of, and for generating random vectors from the multivariate normal and multivariate t distributions. It provides functions similar in scope to those of the package 'mvtnorm', but with some differences; one of these is that probabilities are computed via a non-Monte Carlo method.

Diff between mnormt versions 1.3-2 dated 2009-01-30 and 1.3-3 dated 2009-03-21

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New package vrmlgen with initial version 1.0
Package: vrmlgen
Type: Package
Title: Create plots, charts and graphs for 3D data visualization as VRML files
Version: 1.0
Date: 2009-01-24
Author: Enrico Glaab
Maintainer:
Suggests: misc3d
Description: vrmlgen translates numerical data into 3-dimensional representations like 3D scatter plots, meshes, bar charts and graphs in the Virtual Reality Markup Language (VRML).
License: GNU General Public License
Packaged: Fri Mar 20 17:36:17 2009; egg
Repository: CRAN
Date/Publication: 2009-03-21 08:16:36

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Package timsac updated to version 1.2.1 with previous version 1.1.3 dated 2007-07-07

Author: The Institute of Statistical Mathematics
Title: TIMe Series Analysis and Control package
Description: Time series analysis and control program package TIMSAC.

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Package mi updated to version 0.04-5 with previous version 0.04-4 dated 2009-03-11

Author: Andrew Gelman , Jennifer Hill , Masanao Yajima , Yu-Sung Su , Maria Grazia Pittau
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking

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Package maps updated to version 2.1-0 with previous version 2.0-40 dated 2008-04-17

Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg Enhancements by Thomas P Minka
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata).

Diff between maps versions 2.0-40 dated 2008-04-17 and 2.1-0 dated 2009-03-21

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Package mapdata updated to version 2.1-0 with previous version 2.0-23 dated 2007-10-14

Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or higher-resolution databases.

Diff between mapdata versions 2.0-23 dated 2007-10-14 and 2.1-0 dated 2009-03-21

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Package ccems updated to version 1.02 with previous version 1.01 dated 2009-03-14

Author: Tom Radivoyevitch
Title: Combinatorially Complex Equilibrium Model Selection
Description: Dissociation constants of quasi-equilibriums of enzymes and protein-ligand binding equilibriums in general are systematically scanned though possibilities of being infinity and/or equal to others. The automatically generated space of models is then fitted to data.

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Fri, 20 Mar 2009

Package survival updated to version 2.35-3 with previous version 2.35-2 dated 2009-03-20

Author: Terry Therneau, original R port by Thomas Lumley
Title: Survival analysis, including penalised likelihood.
Description: survival analysis: descriptive statistics, two-sample tests, parametric accelerated failure models, Cox model. Delayed entry (truncation) allowed for all models; interval censoring for parametric models. Case-cohort designs.

Diff between survival versions 2.35-2 dated 2009-03-20 and 2.35-3 dated 2009-03-20

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Package survival updated to version 2.35-2 with previous version 2.34-1 dated 2008-04-02

Author: Terry Therneau, original R port by Thomas Lumley
Title: Survival analysis, including penalised likelihood.
Description: survival analysis: descriptive statistics, two-sample tests, parametric accelerated failure models, Cox model. Delayed entry (truncation) allowed for all models; interval censoring for parametric models. Case-cohort designs.

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 survival-2.35-2/survival/man/survfit.coxph.Rd         |only
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 survival-2.35-2/survival/man/survival-internal.Rd     |    7 
 survival-2.35-2/survival/man/survobrien.Rd            |   62 +-
 survival-2.35-2/survival/man/survreg.Rd               |  103 ++--
 survival-2.35-2/survival/man/survreg.control.Rd       |   16 
 survival-2.35-2/survival/man/survreg.distributions.Rd |  102 ++--
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 survival-2.35-2/survival/src/agexact.c                |   18 
 survival-2.35-2/survival/src/agfit3.c                 |   48 +
 survival-2.35-2/survival/src/agfit5.c                 |   99 ++--
 survival-2.35-2/survival/src/agmart.c                 |    6 
 survival-2.35-2/survival/src/agmart2.c                |    8 
 survival-2.35-2/survival/src/agscore.c                |   10 
 survival-2.35-2/survival/src/agsurv1.c                |   12 
 survival-2.35-2/survival/src/agsurv2.c                |   52 +-
 survival-2.35-2/survival/src/agsurv3.c                |   36 -
 survival-2.35-2/survival/src/chinv2.c                 |    3 
 survival-2.35-2/survival/src/chinv3.c                 |    2 
 survival-2.35-2/survival/src/cholesky2.c              |    3 
 survival-2.35-2/survival/src/cholesky3.c              |    2 
 survival-2.35-2/survival/src/chsolve2.c               |    3 
 survival-2.35-2/survival/src/chsolve3.c               |    2 
 survival-2.35-2/survival/src/cox_Rcallback.c          |    2 
 survival-2.35-2/survival/src/coxdetail.c              |   40 +
 survival-2.35-2/survival/src/coxfit2.c                |   26 -
 survival-2.35-2/survival/src/coxfit5.c                |   73 +--
 survival-2.35-2/survival/src/coxmart.c                |    9 
 survival-2.35-2/survival/src/coxph_wtest.c            |    4 
 survival-2.35-2/survival/src/coxscho.c                |    9 
 survival-2.35-2/survival/src/coxscore.c               |   11 
 survival-2.35-2/survival/src/dmatrix.c                |    4 
 survival-2.35-2/survival/src/doloop.c                 |    3 
 survival-2.35-2/survival/src/pyears1.c                |   50 +-
 survival-2.35-2/survival/src/pyears2.c                |   44 +
 survival-2.35-2/survival/src/pyears3.c                |   33 -
 survival-2.35-2/survival/src/pystep.c                 |   11 
 survival-2.35-2/survival/src/survConcordance.c        |only
 survival-2.35-2/survival/src/survS.h                  |   78 ++-
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 survival-2.35-2/survival/src/survproto.h              |  359 ++++++--------
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 352 files changed, 2688 insertions(+), 2112 deletions(-)

More information about survival at CRAN
Permanent link

Package vowels updated to version 1.0-1 with previous version 1.0 dated 2009-02-16

Author: Tyler Kendall and Erik R. Thomas
Title: Vowel Manipulation, Normalization, and Plotting
Description: vowels is an R package for the manipulation, normalization, and plotting of phonetic and sociophonetic vowel formant data. vowels is the backend for the NORM website.

Diff between vowels versions 1.0 dated 2009-02-16 and 1.0-1 dated 2009-03-20

 DESCRIPTION           |   12 ++++++++----
 R/vowels.R            |    2 +-
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 3 files changed, 11 insertions(+), 7 deletions(-)

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Package stinepack updated to version 1.3 with previous version 1.2 dated 2008-08-21

Author: Tomas Johannesson & Halldor Bjornsson, Icelandic Met. Office; Gabor Grothendieck
Title: Stineman, a consistently well behaved method of interpolation
Description: A consistently well behaved method of interpolation based on piecewise rational functions using Stineman's algorithm

Diff between stinepack versions 1.2 dated 2008-08-21 and 1.3 dated 2009-03-20

 DESCRIPTION        |   12 ++++++++----
 R/parabolaSlopes.R |    4 +++-
 2 files changed, 11 insertions(+), 5 deletions(-)

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Package rscproxy updated to version 1.2-0 with previous version 1.0-12 dated 2008-10-30

Author: Thomas Baier
Title: statconn: provides portable C-style interface to R (StatConnector)
Description: rscproxy library provides an interface to R used by third party applications, most notable, but not limited to, statconnDCOM, ROOo and other systems.

Diff between rscproxy versions 1.0-12 dated 2008-10-30 and 1.2-0 dated 2009-03-20

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New package rbenchmark with initial version 0.1
Package: rbenchmark
Type: Package
Title: Benchmarking routine for R
Version: 0.1
Date: 2009-03-19
Author: Wacek Kusnierczyk
Maintainer: Wacek Kusnierczyk
Description: rbenchmark is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.
License: GPL (>= 2)
LazyLoad: yes
URL: http://rbenchmark.googlecode.com
Packaged: Thu Mar 19 14:43:44 2009; waku
Repository: CRAN
Date/Publication: 2009-03-20 07:48:45

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Thu, 19 Mar 2009

Package AER updated to version 1.1-2 with previous version 1.1-1 dated 2009-03-08

Author: Christian Kleiber, Achim Zeileis
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette for a package overview.)

Diff between AER versions 1.1-1 dated 2009-03-08 and 1.1-2 dated 2009-03-19

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Package spuRs updated to version 1.0.2 with previous version 1.0.1 dated 2009-03-15

Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Title: Functions and Datasets for "An Introduction to Scientific Programming and Simulation, Using R".
Description: This package provides functions and datasets from the book "An Introduction to Scientific Programming and Simulation, Using R".

Diff between spuRs versions 1.0.1 dated 2009-03-15 and 1.0.2 dated 2009-03-19

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Package plotrix updated to version 2.5-4 with previous version 2.5-3 dated 2009-03-16

Author: Jim Lemon,Ben Bolker,Sander Oom, Eduardo Klein,Barry Rowlingson, Hadley Wickham,Anupam Tyagi, Olivier Eterradossi,Gabor Grothendieck, Michael Toews,John Kane,Mike Cheetham, Rolf Turner,Carl Witthoft,Julian Stander, Thomas Petzoldt,Remko Duursma,Elisa Biancotto, Ofir Levy
Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling functions.

Diff between plotrix versions 2.5-3 dated 2009-03-16 and 2.5-4 dated 2009-03-19

 DESCRIPTION        |    6 +++---
 R/dotplot.mtb.R    |    1 -
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New package automap with initial version 1.0-0
Package: automap
Version: 1.0-0
Date: 2009/03/19
Title: Automatic interpolation package
Author: Paul Hiemstra
Maintainer: Paul Hiemstra
Description: This package performs an automatic interpolation by automatically estimating the variogram and then calling gstat.
Depends: R (>= 2.4.0), methods, sp (>= 0.9-4), gstat (>= 0.9-58)
Imports: lattice
License: GPL
Packaged: Thu Mar 19 11:13:17 2009; hiemstra
Repository: CRAN
Date/Publication: 2009-03-19 12:52:43

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Package Rsymphony updated to version 0.1-8 with previous version 0.1-7 dated 2009-02-06

Author: Reinhard Harter, Kurt Hornik and Stefan Theussl
Title: Symphony in R
Description: An R interface to the SYMPHONY MILP solver (version 5.1.10).

Diff between Rsymphony versions 0.1-7 dated 2009-02-06 and 0.1-8 dated 2009-03-19

 DESCRIPTION     |   13 ++++++++-----
 configure       |   13 ++++++++++---
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Package rtv updated to version 0.2.0 with previous version 0.1.0 dated 2009-02-08

Author: Charlotte Maia
Title: Random Time Variable Objects
Description: An R package for conveniently representing and manipulating realisations of random time variables.

Diff between rtv versions 0.1.0 dated 2009-02-08 and 0.2.0 dated 2009-03-19

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Package picante updated to version 0.6-1 with previous version 0.6-0 dated 2009-02-25

Author: Steven Kembel , David Ackerly , Simon Blomberg , Peter Cowan , Matthew Helmus , Helene Morlon , Campbell Webb
Title: R tools for integrating phylogenies and ecology
Description: Phylocom integration, community analyses, null-models, traits and evolution in R

Diff between picante versions 0.6-0 dated 2009-02-25 and 0.6-1 dated 2009-03-19

 DESCRIPTION             |   18 +++++++++++++-----
 R/color.plot.phylo.R    |    4 ++--
 R/cor.table.R           |   23 ++++++++++++-----------
 R/phylodiversity.R      |    2 +-
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 9 files changed, 44 insertions(+), 28 deletions(-)

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Package phmm updated to version 0.5 with previous version 0.4 dated 2009-03-16

Author: Michael Donohue, Ronghui Xu
Title: Proportional Hazards Mixed-effects Model (PHMM)
Description: Fits proportional hazards model incorporating random effects using an EM agorithm using Markov Chain Monte Carlo at E-step.

Diff between phmm versions 0.4 dated 2009-03-16 and 0.5 dated 2009-03-19

 phmm-0.4/phmm/INDEX.txt               |only
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 phmm-0.5/phmm/man/phmm.cond.loglik.Rd |    2 +-
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New package mixRasch with initial version 0.1
Package: mixRasch
Type: Package
Title: Mixture Rasch Models with JMLE
Version: 0.1
Date: 2009-03-13
Author: John T. Willse
Maintainer: John T. Willse
Description: Estimates mixture Rasch models, including the dichotomous Rash model, the rating scale model, and the partial credit model.
License: GPL version 2 or newer
Packaged: Wed Mar 18 14:32:53 2009; jtwillse
Repository: CRAN
Date/Publication: 2009-03-19 08:02:25

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Package DiagnosisMed updated to version 0.1.2.3 with previous version 0.1.2.1 dated 2009-03-06

Author: Pedro Brasil
Title: Diagnostic test accuracy evaluation for medical professionals.
Description: DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is - or soon will be - able to estimate sample size for common situations in diagnostic test accuracy, estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different analysis strategies into measures commonly used by health professionals.

Diff between DiagnosisMed versions 0.1.2.1 dated 2009-03-06 and 0.1.2.3 dated 2009-03-19

 DESCRIPTION |   32 +++++++++++++++++++++-----------
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 3 files changed, 29 insertions(+), 18 deletions(-)

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Wed, 18 Mar 2009

New package Animal with initial version 1.0
Package: Animal
Type: Package
Title: Analyze time-coded behavioral observations
Version: 1.0
Date: 2008-12-18
Author: Matti Pastell
Maintainer: Matti Pastell
Description: A set of functions to analyze time-coded animal behavior data. The package is designed to be used with data files from CowLog (An Open source software for coding behaviors from digital video), but it can be used with any data file with similar format.
License: GPL (>=3)
LazyLoad: yes
Repository: CRAN
Packaged: Wed Mar 18 11:49:24 2009; mpastell
Date/Publication: 2009-03-18 12:48:31

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New package metacor with initial version 1.0
Package: metacor
Type: Package
Title: Meta-analysis of correlation coefficients
Version: 1.0
Date: 2009-03-17
Author: Etienne Laliberte
Maintainer: Etienne Laliberte
Description: Implement the DerSimonian-Laird (DSL) and Olkin-Pratt (OP) meta-analytical approaches with correlation coefficients as effect sizes.
License: GPL-2
LazyLoad: yes
Lazydata: yes
Depends: R (>= 2.8.0), rmeta, gsl
Keyword: meta-analysis
Packaged: Wed Mar 18 12:55:42 2009; Etienne
Repository: CRAN
Date/Publication: 2009-03-18 08:21:53

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Tue, 17 Mar 2009

Package mvtnorm updated to version 0.9-5 with previous version 0.9-4 dated 2009-01-21

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

Diff between mvtnorm versions 0.9-4 dated 2009-01-21 and 0.9-5 dated 2009-03-17

 CHANGES                      |    7 ++++++-
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Package mgcv updated to version 1.5-1 with previous version 1.5-0 dated 2009-03-03

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.

Diff between mgcv versions 1.5-0 dated 2009-03-03 and 1.5-1 dated 2009-03-17

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Package clues updated to version 0.3.2 with previous version 0.3.1 dated 2009-02-16

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 geting 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.

Diff between clues versions 0.3.1 dated 2009-02-16 and 0.3.2 dated 2009-03-17

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Package apTreeshape updated to version 1.4-1 with previous version 1.4-0 dated 2007-04-25

Author: Nicolas Bortolussi , Eric Durand , Michael Blum , Olivier Francois
Title: Analyses of Phylogenetic Treeshape
Description: apTreeshape is mainly dedicated to simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily.

Diff between apTreeshape versions 1.4-0 dated 2007-04-25 and 1.4-1 dated 2009-03-17

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Package MCMCglmm updated to version 1.06 with previous version 1.05 dated 2009-03-06

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

Diff between MCMCglmm versions 1.05 dated 2009-03-06 and 1.06 dated 2009-03-17

 DESCRIPTION           |   17 ++++++++++-------
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Package mice updated to version 1.21 with previous version 1.16 dated 2007-06-25

Author: Stef van Buuren & Karin Groothuis-Oudshoorn
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation of multivariate incomplete data by Fully Conditional Specification

Diff between mice versions 1.16 dated 2007-06-25 and 1.21 dated 2009-03-17

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Package PresenceAbsence updated to version 1.1.3 with previous version 1.1.2 dated 2008-03-28

Author: Elizabeth Freeman .
Title: Presence-Absence Model Evaluation
Description: This package provides a set of functions useful when evaluating the results of presence-absence models. Package includes functions for calculating threshold dependant measures such as confusion matrices, pcc, sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It will calculate optimal threshold choice according to a choice of optimization criteria. It also includes functions to plot the threshold independent ROC curves along with the associated AUC (area under the curve).

Diff between PresenceAbsence versions 1.1.2 dated 2008-03-28 and 1.1.3 dated 2009-03-17

 DESCRIPTION                    |   32 +++++++++++++++++++++-----------
 R/optimal.thresholds.R         |   12 +++++++++---
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 5 files changed, 36 insertions(+), 19 deletions(-)

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Package ISOcodes updated to version 0.2-1 with previous version 0.1-1 dated 2008-04-27

Author: Christian Buchta and Kurt Hornik
Title: Selected ISO codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 and ISO 10646 character codes as well as the Unicode data table.

Diff between ISOcodes versions 0.1-1 dated 2008-04-27 and 0.2-1 dated 2009-03-17

 DESCRIPTION                    |   17 +++--
 data/ISO_15924.rda             |binary
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 data/ISO_4217_Historic.rda     |binary
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 data/ISO_639_3_Retirements.rda |binary
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More information about ISOcodes at CRAN
Permanent link

Mon, 16 Mar 2009

New package phmm with initial version 0.4
Package: phmm
Version: 0.4
Date: 2008-12-18
Title: Proportional Hazards with Mixed Model (PHMM)
Author: Ronghui Xu, Michael Donohue
Maintainer: Michael Donohue
Depends: survival
Suggests: lme4
Description: Fits proportional hazards model incorporating random effects using an EM agorithm using Markov Chain Monte Carlo at E-step.
License: GPL-2
Packaged: Mon Mar 16 10:09:32 2009; mdonohue
Repository: CRAN
Date/Publication: 2009-03-16 18:37:41

More information about phmm at CRAN
Permanent link

Package lmom updated to version 1.2 with previous version 1.1 dated 2008-12-30

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 1.1 dated 2008-12-30 and 1.2 dated 2009-03-16

 DESCRIPTION   |   25 ++++++++++++++-----------
 NEWS          |    9 +++++++++
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 man/0-lmom.Rd |    6 +++---
 man/cdfln3.Rd |    2 +-
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 man/lmrp.Rd   |    2 +-
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More information about lmom at CRAN
Permanent link

Package coin updated to version 1.0-2 with previous version 1.0-1 dated 2009-01-09

Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim Zeileis
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.

Diff between coin versions 1.0-1 dated 2009-01-09 and 1.0-2 dated 2009-03-16

 CHANGES                          |    6 +++
 DESCRIPTION                      |   19 +++++++----
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 ToDoList                         |    3 +
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 tests/bugfixes.R                 |   13 ++++++++
 tests/bugfixes.Rout.save         |   63 ++++++++++++++++++++++++++++++++++++++-
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More information about coin at CRAN
Permanent link

Package DPpackage updated to version 1.0-7 with previous version 1.0-6 dated 2008-07-14

Author: Alejandro Jara with contributions from Timothy Hanson , Fernando A. Quintana , Peter Mueller , and Gary L. Rosner .
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, 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.

Diff between DPpackage versions 1.0-6 dated 2008-07-14 and 1.0-7 dated 2009-03-16

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More information about DPpackage at CRAN
Permanent link

Package plotrix updated to version 2.5-3 with previous version 2.5-2 dated 2009-02-18

Author: Jim Lemon,Ben Bolker,Sander Oom, Eduardo Klein,Barry Rowlingson, Hadley Wickham,Anupam Tyagi, Olivier Eterradossi,Gabor Grothendieck, Michael Toews,John Kane,Mike Cheetham, Rolf Turner,Carl Witthoft,Julian Stander, Thomas Petzoldt,Remko Duursma,Elisa Biancotto, Ofir Levy
Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling functions.

Diff between plotrix versions 2.5-2 dated 2009-02-18 and 2.5-3 dated 2009-03-16

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More information about plotrix at CRAN
Permanent link

Package clinsig updated to version 1.0-1 with previous version 1.0 dated 2009-01-20

Author: Jim Lemon ,
Title: Clinical significance functions.
Description: Functions for calculating clinical significance.

Diff between clinsig versions 1.0 dated 2009-01-20 and 1.0-1 dated 2009-03-16

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Permanent link

Package IDPmisc updated to version 1.0.01 with previous version 0.9.9 dated 2008-07-28

Author: Andreas Ruckstuhl, Thomas Unternaehrer, Rene Locher
Title: Utilities of Institute of Data Analyses and Process Design (www.idp.zhaw.ch)
Description: The IDPmisc package contains different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra.

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Package rattle updated to version 2.4.47 with previous version 2.4.45 dated 2009-03-14

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 2.4.45 dated 2009-03-14 and 2.4.47 dated 2009-03-16

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More information about rattle at CRAN
Permanent link

Package RSEIS updated to version 2.1-4 with previous version 2.1-1 dated 2009-02-06

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 2.1-1 dated 2009-02-06 and 2.1-4 dated 2009-03-16

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Package HH updated to version 2.1-25 with previous version 2.1-24 dated 2009-02-28

Author: Richard M. Heiberger
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Springer, ISBN 0-387-40270-5). This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The authors demonstrate how to analyze data---showing code, graphics, and accompanying computer listings---for all the methods they cover. They emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises.

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Sun, 15 Mar 2009

Package spuRs updated to version 1.0.1 with previous version 1.0 dated 2009-03-13

Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Title: Functions and Datasets for "An Introduction to Scientific Programming and Simulation, Using R".
Description: This package provides functions and datasets from the book "An Introduction to Scientific Programming and Simulation, Using R".

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Package rgl updated to version 0.84 with previous version 0.83-3 dated 2009-02-24

Author: Daniel Adler , Duncan Murdoch
Title: 3D visualization device system (OpenGL)
Description: 3D visualization device (OpenGL)

Diff between rgl versions 0.83-3 dated 2009-02-24 and 0.84 dated 2009-03-15

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Permanent link

New package SpectralGEM with initial version 0.1
Package: SpectralGEM
Version: 0.1
Date: 2009-02-07
Title: Discovering Genetic Ancestry Using Spectral Graph Theory
Author: Ann Lee, Diana Luca, Bert Klei, Bernie Devlin, Kathryn Roeder
Maintainer: Jing Wu
Depends: survival, optmatch, R (>= 2.0)
Description: Discovering Genetic Ancestry Using Spectral Graph Theory
License: GPL-2
Packaged: Sat Mar 14 22:17:41 2009; jwu
Repository: CRAN
Date/Publication: 2009-03-15 09:39:09

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Sat, 14 Mar 2009

New package TeachingSampling with initial version 0.7.6
Package: TeachingSampling
Type: Package
Title: Sampling designs and parameter estimation in finite population
License: GPL (>= 2)
Version: 0.7.6
Date: 2009-03-05
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas
Depends: R (>= 2.6.0)
Description: Foundations of inference in survey sampling
URL: http://www.predictive.wordpress.com/stats/
Encoding: latin1
Packaged: Sat Mar 14 10:54:14 2009; User
Repository: CRAN
Date/Publication: 2009-03-14 19:47:03

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Package OAIHarvester updated to version 0.0-3 with previous version 0.0-2 dated 2009-03-05

Author: Kurt Hornik
Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0.

Diff between OAIHarvester versions 0.0-2 dated 2009-03-05 and 0.0-3 dated 2009-03-14

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Package ccems updated to version 1.01 with previous version 1.0 dated 2009-03-06

Author: Tom Radivoyevitch
Title: Combinatorially Complex Equilibrium Model Selection
Description: Dissociation constants of quasi-equilibriums of enzymes and protein-ligand binding equilibriums in general are systematically scanned though possibilities of being infinity and/or equal to others. The automatically generated space of models is then fitted to data.

Diff between ccems versions 1.0 dated 2009-03-06 and 1.01 dated 2009-03-14

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New package aspect with initial version 0.8-0
Package: aspect
Type: Package
Title: Aspects of Multivariables
Version: 0.8-0
Date: 2008-03-13
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw
Description: This package consists of two main functions: The first function is corAspect() performs (optimal) scaling by maximizing an aspect (i.e. target function such as sum eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. The second function is lineals() which performs scaling by mimimization a non-correlational aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as SEM. A platform including related PsychoR packages is provided on R-forge.
License: GPL
URL: http://r-forge.r-project.org/projects/psychor/
LazyLoad: yes
Packaged: Fri Mar 13 15:44:58 2009; admin
Repository: CRAN
Date/Publication: 2009-03-14 11:08:19

More information about aspect at CRAN
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Package rattle updated to version 2.4.45 with previous version 2.4.41 dated 2009-03-04

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.

Diff between rattle versions 2.4.41 dated 2009-03-04 and 2.4.45 dated 2009-03-14

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 man/audit.Rd                    |   81 ++
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Package fuzzyOP updated to version 1.1 with previous version 1.0 dated 2008-07-07

Author: Semagul Aklan, Emine Altindas, Rabiye Macit, Senay Umar, Hatice Unal
Title: Fuzzy numbers and the main mathematical operations
Description: This package contains functions which allow the depiction of fuzzy numbers. Besides, the main arithmetic operations are applied to fuzzy numbers and the extension principle for continuous functions can be applied and plotted.

Diff between fuzzyOP versions 1.0 dated 2008-07-07 and 1.1 dated 2009-03-14

 DESCRIPTION            |   29 +++++++++++++++++------------
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 man/fuzzynumber.Rd     |    2 +-
 man/fuzzypower.Rd      |    2 +-
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 man/fuzzyscalar.Rd     |    2 +-
 man/fuzzysum.Rd        |    2 +-
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Package TRIANG updated to version 1.1 with previous version 1.0 dated 2009-03-08

Author: Tristan Senga Kiess\'{e}, Silvio S. Zocchi, C\'{e}lestin C. Kokonendji
Title: Discrete triangular distributions
Description: This is a package for discrete triangular distributions which complete the classical discrete distributions like binomial, Poisson and Negative binomial.

Diff between TRIANG versions 1.0 dated 2009-03-08 and 1.1 dated 2009-03-14

 DESCRIPTION                  |   17 ++++---
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Fri, 13 Mar 2009

New package spuRs with initial version 1.0
Package: spuRs
Type: Package
Title: Functions and Datasets for "An Introduction to Scientific Programming and Simulation, Using R".
Version: 1.0
Date: 2008-09-04
Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Maintainer: Andrew Robinson
Depends: MASS
Description: This package provides functions and datasets from the book "An Introduction to Scientific Programming and Simulation, Using R".
License: GPL-3
LazyLoad: yes
Packaged: Fri Mar 13 11:40:42 2009; hornik
Repository: CRAN
Date/Publication: 2009-03-13 10:46:47

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New package spcosa with initial version 0.1-1
Package: spcosa
Type: Package
Title: Spatial Coverage Sampling
Version: 0.1-1
Date: 2009-03-13
Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Maintainer: Dennis Walvoort
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means.
Depends: R (>= 2.8.0), rJava (>= 0.6-1), methods, ggplot2 (>= 0.8.1), rgdal
Suggests: classGraph, gpclib, gstat, rgl
Imports: sp (>= 0.9-28)
SystemRequirements: Java (>= 6.0)
License: GPL (>= 3)
LazyLoad: yes
Collate: class_Stratification.R class_CompactStratification.R class_CompactStratificationEqualArea.R class_CompactStratificationPriorPoints.R class_SamplingPattern.R class_SamplingPatternPurposive.R class_SamplingPatternCentroids.R class_SamplingPatternPriorPoints.R class_SamplingPatternRandom.R class_SamplingPatternRandomSamplingUnits.R class_SamplingPatternRandomComposite.R class_Statistic.R class_SpatialMean.R class_SamplingVariance.R class_StandardError.R class_SpatialVariance.R class_SpatialCumulativeDistributionFunction.R generic_estimate.R generic_getArea.R generic_getRelativeArea.R generic_getAttributes.R generic_getCellSize.R generic_getCentroid.R generic_getSampleSize.R generic_getNumberOfCells.R generic_getNumberOfStrata.R generic_getObjectiveFunctionValue.R generic_stratify.R generic_plot.R method_estimate-SamplingVariance-CompactStratification-SamplingPatternRandom-data.frame.R method_estimate-SamplingVariance-CompactStratificationEqualArea-SamplingPatternRandomComposite-data.frame.R method_estimate-SpatialCumulativeDistributionFunction-CompactStratification-SamplingPatternRandom-data.frame.R method_estimate-SpatialMean-CompactStratification-SamplingPatternRandom-data.frame.R method_estimate-SpatialMean-CompactStratificationEqualArea-SamplingPatternRandomComposite-data.frame.R method_estimate-SpatialVariance-CompactStratification-SamplingPatternRandom-data.frame.R method_estimate-StandardError-CompactStratification-SamplingPatternRandom-data.frame.R method_estimate-character-CompactStratificationEqualArea-SamplingPatternRandomComposite-data.frame.R method_estimate-character-CompactStratification-SamplingPatternRandomSamplingUnits-data.frame.R method_getArea-CompactStratification.R method_getRelativeArea-CompactStratification.R method_getCellSize-CompactStratification.R method_getCentroid-CompactStratification.R method_getNumberOfCells-CompactStratification.R method_getNumberOfStrata-CompactStratification.R method_getObjectiveFunctionValue-CompactStratification.R method_getSampleSize-SamplingPattern.R method_getSampleSize-SamplingPatternRandomComposite.R method_initialize-CompactStratification.R method_initialize-CompactStratificationPriorPoints.R method_stratify-SpatialPixels.R method_stratify-SpatialPolygons.R method_plot-CompactStratification.R method_plot-SamplingPattern.R method_plot-SamplingPatternPriorPoints.R method_plot-SamplingPatternRandomComposite.R method_plot-CompactStratification-SamplingPattern.R method_plot-CompactStratification-SamplingPatternPriorPoints.R method_plot-CompactStratification-SamplingPatternRandomComposite.R method_spsample_CompactStratificationEqualArea-numeric-character.R method_spsample_CompactStratification-missing-missing.R method_spsample_CompactStratification-numeric-missing.R method_spsample_CompactStratificationPriorPoints-missing.R method_setAs_SamplingPattern-data.frame.R method_setAs_SamplingPattern-SpatialPoints.R method_setAs_SamplingPatternRandomComposite-data.frame.R method_setAs_SamplingPatternRandomComposite-SpatialPointsDataFrame.R method_setAs_CompactStratification-data.frame.R method_setAs_CompactStratification-SpatialPixels.R method_setAs_CompactStratification-SpatialPixelsDataFrame.R method_show-Stratification.R method_show-SamplingPattern.R method_show-Statistic.R onLoad.R
Packaged: Fri Mar 13 11:46:09 2009; walvo001
Repository: CRAN
Date/Publication: 2009-03-13 11:04:30

More information about spcosa at CRAN
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Package biclust updated to version 0.7.1 with previous version 0.5 dated 2008-02-04

Author: Sebastian Kaiser, Rodrigo Santamaria, Roberto Theron, Luis Quintales and Friedrich Leisch.
Title: BiCluster Algorithms
Description: The main function biclust provides several algorithms to find biclusters in two-dimensional data: Cheng and Church, Spectral, Plaid Model, Xmotifs and Bimax. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.

Diff between biclust versions 0.5 dated 2008-02-04 and 0.7.1 dated 2009-03-13

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Package RcmdrPlugin.survival updated to version 0.7-1 with previous version 0.7-0 dated 2009-02-20

Author: John Fox
Title: R Commander Plug-in for the survival Package
Description: This package provides an R Commander plug-in for the survival package, with dialogs for Cox models, parametric survival regression models, estimation of survival curves, and testing for differences in survival curves, along with data-management facilities and a variety of tests, diagnostics and graphs.

Diff between RcmdrPlugin.survival versions 0.7-0 dated 2009-02-20 and 0.7-1 dated 2009-03-13

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Package Rcmdr updated to version 1.4-8 with previous version 1.4-7 dated 2009-01-08

Author: John Fox , with contributions from Michael Ash, Theophilius Boye, Stefano Calza, Andy Chang, Philippe Grosjean, Richard Heiberger, G. Jay Kerns, Renaud Lancelot, Matthieu Lesnoff, Samir Messad, Martin Maechler, Duncan Murdoch, Erich Neuwirth, Dan Putler, Brian Ripley, Miroslav Ristic, and Peter Wolf.
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.

Diff between Rcmdr versions 1.4-7 dated 2009-01-08 and 1.4-8 dated 2009-03-13

 DESCRIPTION              |   40 +++++++++++++--------
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Package rgenoud updated to version 5.5-1 with previous version 5.4-7 dated 2008-01-07

Author: Walter R. Mebane, Jr. , Jasjeet Singh Sekhon
Title: R version of GENetic Optimization Using Derivatives
Description: A genetic algorithm plus derivative optimizer

Diff between rgenoud versions 5.4-7 dated 2008-01-07 and 5.5-1 dated 2009-03-13

 DESCRIPTION           |   14 +-
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Package pomp updated to version 0.22-6 with previous version 0.22-5 dated 2009-02-04

Author: Aaron A. King, Edward L. Ionides, Carles Martinez 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 0.22-5 dated 2009-02-04 and 0.22-6 dated 2009-03-13

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Package ouch updated to version 2.5-4 with previous version 2.5-3 dated 2009-01-30

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 2.5-3 dated 2009-01-30 and 2.5-4 dated 2009-03-13

 DESCRIPTION               |   19 ++++++++++++-------
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Package gWidgets updated to version 0.0-35 with previous version 0.0-32 dated 2008-12-18

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

Diff between gWidgets versions 0.0-32 dated 2008-12-18 and 0.0-35 dated 2009-03-13

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Package dplR updated to version 1.1.7 with previous version 1.1.6 dated 2009-01-01

Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some standard tree-ring analyses.

Diff between dplR versions 1.1.6 dated 2009-01-01 and 1.1.7 dated 2009-03-13

 DESCRIPTION  |   27 +++++++++++++++------------
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Package Matrix updated to version 0.999375-22 with previous version 0.999375-21 dated 2009-02-15

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 0.999375-21 dated 2009-02-15 and 0.999375-22 dated 2009-03-13

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Thu, 12 Mar 2009

Package foreign updated to version 0.8-34 with previous version 0.8-33 dated 2009-02-18

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

Diff between foreign versions 0.8-33 dated 2009-02-18 and 0.8-34 dated 2009-03-12

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Package boot updated to version 1.2-36 with previous version 1.2-35 dated 2009-01-04

Author: S original by Angelo Canty . R port by Brian Ripley .
Title: Bootstrap R (S-Plus) Functions (Canty)
Description: functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Applications" by A. C. Davison and D. V. Hinkley (1997, CUP).

Diff between boot versions 1.2-35 dated 2009-01-04 and 1.2-36 dated 2009-03-12

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Package sda updated to version 1.1.0 with previous version 1.0.3 dated 2008-12-08

Author: Miika Ahdesmaki and Korbinian Strimmer
Title: Shrinkage Discriminant Analysis and Feature Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with feature selection. The classifier is trained using Stein-type shrinkage estimators and features are ranked using correlation-adjusted t-scores. Feature selection is controlled using false non-discovery rates or higher criticism scores.

Diff between sda versions 1.0.3 dated 2008-12-08 and 1.1.0 dated 2009-03-12

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Package rngwell19937 updated to version 0.5-1 with previous version 0.5-0 dated 2009-03-05

Author: Petr Savicky
Title: WELL19937a random number generator implemented with 53 bit output
Description: Random number generator WELL19937a by F. Panneton, P. L'Ecuyer and M. Matsumoto with initialization using MRG32k5a by P. L'Ecuyer. WELL19937a is of similar type as Mersenne Twister (MT), is slightly slower than MT, has better equidistribution than MT and faster recovery from states with prevailing zeros. The output function may be set to provide numbers with 53 or 32 random bits.

Diff between rngwell19937 versions 0.5-0 dated 2009-03-05 and 0.5-1 dated 2009-03-12

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Package penalized updated to version 0.9-23 with previous version 0.9-22 dated 2008-09-29

Author: Jelle Goeman
Title: L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model
Description: A package for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.

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New package jointDiag with initial version 0.1
Package: jointDiag
Version: 0.1
Date: 2009-02-20
Title: Joint Approximate Diagonalization of a set of square matrices
Author: Cedric Gouy-Pailler from original code by Antoine Souloumiac (J_Di), Dinh-Tuan Pham (jadiag and lscjadiag), Marco Congedo (lscjadiag), Petr Tichavky (uwedge), Andreas Ziehe (ffdiag), Roland Vollgraf (qdiag)
Maintainer: Cedric Gouy-Pailler
Depends:
Suggests:
Description: Different algorithms to perform approximate joint diagonalization of a finite set of square matrices. The algorithms have been provided by different authors (see list above). Depending on the algorithm, orthogonal or non-orthogonal diagonalizer is found.
License: GPL (>= 2)
URL: http://www.r-project.org http://www.lis.inpg.fr/pages_perso/gouypailler/
Packaged: Thu Mar 12 11:33:50 2009; gouypailler
Repository: CRAN
Date/Publication: 2009-03-12 20:07:01

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Package HyperbolicDist updated to version 0.5-3 with previous version 0.5-2 dated 2008-04-29

Author: David Scott
Title: The hyperbolic distribution
Description: This package provides functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, including fitting of the hyperbolic to data.

Diff between HyperbolicDist versions 0.5-2 dated 2008-04-29 and 0.5-3 dated 2009-03-12

 ChangeLog                     |   40 ++++++++++++++-
 DESCRIPTION                   |   38 ++++++++------
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New package Oncotree with initial version 0.3
Package: Oncotree
Type: Package
Title: Estimating oncogenetic trees
Version: 0.3
Date: 2009-03-10
Author: Aniko Szabo, Lisa Pappas
Maintainer: Aniko Szabo
Depends: R (>= 2.3.1), boot
Suggests: lattice
Description: Contains functions to construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis.
License: GPL 2 or newer
Packaged: Wed Mar 11 16:03:27 2009; aszabo
Repository: CRAN
Date/Publication: 2009-03-12 09:28:15

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Wed, 11 Mar 2009

Package mi updated to version 0.04-4 with previous version 0.04-3 dated 2009-03-11

Author: Andrew Gelman , Jennifer Hill , Masanao Yajima , Yu-Sung Su , Maria Grazia Pittau
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking

Diff between mi versions 0.04-3 dated 2009-03-11 and 0.04-4 dated 2009-03-11

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 4 files changed, 32 insertions(+), 26 deletions(-)

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Package bipartite updated to version 0.85 with previous version 0.84 dated 2009-02-25

Author: Carsten F. Dormann and Bernd Gruber, with additional code from Jochen Fruend, also based on C-code developed by Nils Bluethgen and by Miguel Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological indices.
Description: See bipartite-package for more details.

Diff between bipartite versions 0.84 dated 2009-02-25 and 0.85 dated 2009-03-11

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 4 files changed, 57 insertions(+), 25 deletions(-)

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Package R2jags updated to version 0.01-21 with previous version 0.01-20 dated 2009-03-10

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 0.01-20 dated 2009-03-10 and 0.01-21 dated 2009-03-11

 CHANGELOG        |    4 ++++
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Package CCA updated to version 1.2 with previous version 1.1 dated 2007-03-20

Author: Ignacio Gonzlez, Sbastien Djean
Title: Canonical correlation analysis
Description: The package provide a set of functions that extend the cancor function with new numerical and graphical outputs. It also include a regularized extension of the cannonical correlation analysis to deal with datasets with more variables than observations.

Diff between CCA versions 1.1 dated 2007-03-20 and 1.2 dated 2009-03-11

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Package ks updated to version 1.6.2 with previous version 1.6.1 dated 2009-02-16

Author: Tarn Duong
Title: Kernel smoothing
Description: Kernel density estimators and kernel discriminant analysis for multivariate data

Diff between ks versions 1.6.1 dated 2009-02-16 and 1.6.2 dated 2009-03-11

 DESCRIPTION      |   17 ++++++++++-------
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 inst/doc/kde.pdf |binary
 4 files changed, 22 insertions(+), 18 deletions(-)

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Package clusterSim updated to version 0.36-4 with previous version 0.36-3 dated 2008-10-14

Author: Marek Walesiak Andrzej Dudek
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

Diff between clusterSim versions 0.36-3 dated 2008-10-14 and 0.36-4 dated 2009-03-11

 DESCRIPTION  |   50 +++++++++++++++++++++-----------------------------
 R/index.G1.r |   14 +++++++++++---
 R/index.H.r  |   19 ++++++++++++++++---
 3 files changed, 48 insertions(+), 35 deletions(-)

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New package BayesX with initial version 0.2
Package: BayesX
Type: Package
Title: R Utilities Accompanying the Software Package BayesX
Version: 0.2
Date: 2009-03-10
Author: Thomas Kneib, Felix Heinzl, Andreas Brezger, Daniel Sabanes Bove
Maintainer: Thomas Kneib
Description: This package provides functionality for exploring and visualising estimation results obtained with the software package BayesX for structured additive regression. It also provides functions that allow to read, write and manipulate map objects that are required in spatial analyses performed with BayesX.
Depends: akima, shapefiles
Imports: sp, colorspace, coda, splines
Suggests: spdep
LazyLoad: yes
License: GPL-2
Packaged: Wed Mar 11 11:11:33 2009; tkneib
Repository: CRAN
Date/Publication: 2009-03-11 17:02:02

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Package fbati updated to version 0.6.2 with previous version 0.6.1 dated 2009-03-10

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 0.6.1 dated 2009-03-10 and 0.6.2 dated 2009-03-11

 DESCRIPTION    |   13 ++-
 src/cgFbat.cpp |  187 ++++++++++++++++++++++++++++-----------------------------
 2 files changed, 103 insertions(+), 97 deletions(-)

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Package ucminf updated to version 1.0-5 with previous version 1.0-4 dated 2009-03-03

Author: Hans Bruun Nielsen and Stig Bousgaard Mortensen
Title: General-purpose unconstrained non-linear optimization
Description: An algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of 'ucminf' is designed for easy interchange with 'optim'.

Diff between ucminf versions 1.0-4 dated 2009-03-03 and 1.0-5 dated 2009-03-11

 DESCRIPTION   |    6 +++---
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 man/ucminf.Rd |    6 ++++--
 3 files changed, 15 insertions(+), 8 deletions(-)

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Package mi updated to version 0.04-3 with previous version 0.04-2 dated 2009-03-06

Author: Andrew Gelman , Jennifer Hill , Masanao Yajima , Yu-Sung Su , Maria Grazia Pittau
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking

Diff between mi versions 0.04-2 dated 2009-03-06 and 0.04-3 dated 2009-03-11

 CHANGELOG                |   10 ++++++++++
 DESCRIPTION              |    6 +++---
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 9 files changed, 94 insertions(+), 71 deletions(-)

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Package gmm updated to version 1.0-4 with previous version 1.0-3 dated 2009-03-09

Author: Pierre Chausse
Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).

Diff between gmm versions 1.0-3 dated 2009-03-09 and 1.0-4 dated 2009-03-11

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Package fgui updated to version 0.3.2 with previous version 0.3.1 dated 2009-02-23

Author: Thomas Hoffmann
Title: Function GUI
Description: Rapidly create a GUI interface for a function you created by automatically creating widgets for arguments of the function. Automatically parses help routines for context-sensative help to these arguments. The interface essentially a wrapper to some tcltk routines to both simplify and facilitate GUI creation. More advanced tcltk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.

Diff between fgui versions 0.3.1 dated 2009-02-23 and 0.3.2 dated 2009-03-11

 DESCRIPTION |   26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

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Package clustvarsel updated to version 1.2 with previous version 1.1 dated 2006-11-30

Author: Nema Dean and Adrian E. Raftery
Title: Variable Selection for Model-Based Clustering
Description: The selection method uses either a greedy search or headlong search. The greedy search at each step either checks all variables not currently included in the set of clustering variables singly for inclusion into the set or checks all variables in the set of clustering variables singly for exclusion.The headlong search only checks until a variable is included or excluded (i.e. does not necessarily check all possible variables for inclusion/exclusion at each step) and any variable with evidence of clustering below a certain level at any stage is removed from consideration for the remainder of the algorithm. Each variable's evidence for being useful to the clustering given the currently selected clustering variables is given by the difference between the BIC for the model with clustering (allowed to vary over 2 to a maximum number of groups and any of the different covariance parameterizations allowed in mclust) using the set of clustering variables including the variable being checked and the sum of BICs for the model with clustering (allowed to vary over 2 to a maximum number of groups and any of the different covariance parameterizations allowed in mclust) using the set of clustering variables without the variable being checked and the model for the variable being checked being conditionally independent of the clustering given the other clustering variables (this is modeled as a regression of the variable being checked on the other clustering variables).

Diff between clustvarsel versions 1.1 dated 2006-11-30 and 1.2 dated 2009-03-11

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Package animation updated to version 1.0-4 with previous version 1.0-3 dated 2009-02-15

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 1.0-3 dated 2009-02-15 and 1.0-4 dated 2009-03-11

 DESCRIPTION         |    8 ++++----
 R/flip.coin.R       |    2 +-
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Package RcmdrPlugin.epack updated to version 1.1-4 with previous version 1.1-3 dated 2008-08-09

Author: Erin Hodgess
Title: Rcmdr plugin for time series
Description: This package provides an Rcmdr "plug-in" based on the time series functions. Contributors: G. Jay Kerns, John Fox, and Richard Heiberger.

Diff between RcmdrPlugin.epack versions 1.1-3 dated 2008-08-09 and 1.1-4 dated 2009-03-11

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Package FrF2 updated to version 0.9 with previous version 0.8 dated 2008-02-17

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; structures and even function names may change in the future.

Diff between FrF2 versions 0.8 dated 2008-02-17 and 0.9 dated 2009-03-11

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Tue, 10 Mar 2009

Package rjags updated to version 1.0.3-8 with previous version 1.0.3-7 dated 2009-03-06

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

Diff between rjags versions 1.0.3-7 dated 2009-03-06 and 1.0.3-8 dated 2009-03-10

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Package pbatR updated to version 2.1.4 with previous version 2.1.2.1 dated 2009-02-23

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 2.1.2.1 dated 2009-02-23 and 2.1.4 dated 2009-03-10

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Package fbati updated to version 0.6.1 with previous version 0.5.2.1 dated 2009-02-23

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.

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Package analogue updated to version 0.6-6 with previous version 0.5-2 dated 2008-05-13

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.

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Package R2jags updated to version 0.01-20 with previous version 0.01-18 dated 2009-03-08

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 0.01-18 dated 2009-03-08 and 0.01-20 dated 2009-03-10

 CHANGELOG        |   13 +++++++++----
 DESCRIPTION      |    8 ++++----
 R/autojags.R     |    6 +++---
 R/jags.R         |   12 +++++++-----
 R/jags2.R        |    2 +-
 R/recompile.R    |    6 +++---
 R/update.R       |    4 ++--
 man/autojags.Rd  |    5 +++--
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 10 files changed, 36 insertions(+), 27 deletions(-)

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Permanent link

Package FracSim updated to version 0.3 with previous version 0.2 dated 2005-12-02

Author: S. Djean and S. Cohen
Title: Simulation of Lvy motions
Description: The functions provided in FracSim perform simulation of one- and two-dimensional fractional and multifractional Lvy motions

Diff between FracSim versions 0.2 dated 2005-12-02 and 0.3 dated 2009-03-10

 DESCRIPTION       |    7 ++++---
 man/fracsim.1d.Rd |    1 +
 man/fracsim.2d.Rd |    3 ++-
 3 files changed, 7 insertions(+), 4 deletions(-)

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Package smacof updated to version 0.9-5 with previous version 0.9-3 dated 2009-02-07

Author: Jan de Leeuw, Patrick Mair
Title: smacof for Multidimensional Scaling.
Description: This package provides the following approaches of multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): Simple smacof on symmetric dissimilarity matrices, smacof for rectangular matrices (unfolding models), smacof with constraints on the configuration, three-way smacof for individual differences (including constraints for idioscal, indscal, and identity), and spherical smacof (primal and dual algorithm). Each of these approaches is implemented in a metric and nonmetric manner including primary, secondary, and tertiary approaches for tie handling.

Diff between smacof versions 0.9-3 dated 2009-02-07 and 0.9-5 dated 2009-03-10

 DESCRIPTION              |    6 +++---
 NAMESPACE                |    2 ++
 R/plot.smacof.R          |    5 ++---
 R/plot.smacofID.r        |    8 +++-----
 R/plot3d.smacof.r        |    2 +-
 R/plot3d.smacofID.r      |    2 +-
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 R/smacofConstraint.R     |   14 ++++++++++----
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 R/smacofRect.R           |   13 +++++++++++--
 R/smacofSphere.dual.R    |   17 +++++++++++++----
 R/smacofSphere.primal.R  |   12 +++++++++---
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 man/plot3d.smacof.rd     |   10 +++++-----
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 man/smacofSphere.dual.rd |    1 +
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New package plotpc with initial version 1.0-1
Package: plotpc
Version: 1.0-1
Title: Plot principal component histograms around a scatter plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
Depends: grid
Description: Plot principal component histograms around a bivariate scatter plot.
License: GPL-3
URL: http://www.milbo.users.sonic.net
Packaged: Tue Mar 10 12:13:51 2009; steve

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New package spatialsegregation with initial version 1.93
Package: spatialsegregation
Type: Package
Title: Segregation measures for multitype spatial point patterns
Version: 1.93
Date: 2009-03-09
Author: Tuomas Rajala
Maintainer: Tuomas Rajala
Suggests:
Depends: spatgraphs (>= 2.0)
Description: Functionals and indices for measuring segregation in multitype spatial point patterns with graph based neighbourhood description. Included indices: Mingling, Shannon, Simpson (also the non-spatial) Included functionals: Mingling, Shannon, Simpson, ISAR. Included neighbourhoods: Geometric, k-nearest neighbours, Gabriel, Delauney.
License: GPL (>= 2.0)
Packaged: Tue Mar 10 09:46:33 2009; tarajala

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Package rpart updated to version 3.1-43 with previous version 3.1-42 dated 2008-10-20

Author: Terry M Therneau and Beth Atkinson . R port by Brian Ripley.
Title: Recursive Partitioning
Description: Recursive partitioning and regression trees

Diff between rpart versions 3.1-42 dated 2008-10-20 and 3.1-43 dated 2009-03-10

 ChangeLog               |    9 +++++++--
 DESCRIPTION             |    6 +++---
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 R/rpart.s               |   12 +++++++++---
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Package ifs updated to version 0.1-3 with previous version 0.1-2 dated 2006-09-19

Author: S. M. Iacus
Title: Iterated Function Systems
Description: Iterated Function Systems

Diff between ifs versions 0.1-2 dated 2006-09-19 and 0.1-3 dated 2009-03-10

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

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Package gss updated to version 1.0-5 with previous version 1.0-4 dated 2009-03-06

Author: Chong Gu
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.

Diff between gss versions 1.0-4 dated 2009-03-06 and 1.0-5 dated 2009-03-10

 ChangeLog   |    6 ++++++
 DESCRIPTION |    4 ++--
 R/rkpk.R    |   16 ++++++++--------
 3 files changed, 16 insertions(+), 10 deletions(-)

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Package VR updated to version 7.2-46 with previous version 7.2-45 dated 2008-12-10

Author: S original by Venables & Ripley. R port by Brian Ripley , following earlier work by Kurt Hornik and Albrecht Gebhardt.
Bundle: VR
Contains: MASS class nnet spatial

Diff between VR versions 7.2-45 dated 2008-12-10 and 7.2-46 dated 2009-03-10

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Package MiscPsycho updated to version 1.4 with previous version 1.3 dated 2008-10-02

Author: Harold C. Doran
Title: Miscellaneous Psychometrics
Description: Computes statistical analyses useful for applied psychometricians

Diff between MiscPsycho versions 1.3 dated 2008-10-02 and 1.4 dated 2009-03-10

 MiscPsycho-1.3/MiscPsycho/inst/doc/Levenshtein.pdf |only
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Package CvM2SL2Test updated to version 0.0-2 with previous version 0.0-1 dated 2008-08-08

Author: Yuanhui Xiao and Ye Cui
Title: Cramer-von Mises Two Sample Tests
Description: The package contains two functions: one computes the Cramer-von Mises two sample test scores, the other cmoputes the exact p-value(s) for given Cramer-von Mises two-sample test score(s) under the assumption that the populations under comparison have the same probability distribution. Like Kolmogorov-Smirnov two-sample test, Cramer-von Mises test is also distribution free. In certain cases, the Cramer-von Mises test is more powerful than the Kolmogorov-Smirnov test, but it is less widely used than the latter.

Diff between CvM2SL2Test versions 0.0-1 dated 2008-08-08 and 0.0-2 dated 2009-03-10

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 NAMESPACE               |    2 +-
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 man/cvmts.test.Rd       |    2 +-
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Mon, 09 Mar 2009

New package AIGIS with initial version 1.0
Package: AIGIS
Type: Package
Title: Areal Interpolation for GIS data
Version: 1.0
Date: 2009-03-06
Author: Benjamin P. Bryant and Anthony Westerling
Maintainer: Bryant
Depends: R (>= 2.5.1), gpclib (>= 1.4)
Description: AIGIS can be used to interpolate spatially associated data onto arbitrary target polygons which lack such data. Version 1.0 of the package is oriented toward convenient interpolation of specific US census data for California, but the tools provided should work for any combination of GIS data source and target polygon, provided appropriate care is taken. Future versions will be aimed at facilitating more general applications.
License: GPL-3
Packaged: Mon Mar 9 10:24:13 2009; bryant

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Package micEcon updated to version 0.5-14 with previous version 0.5-12 dated 2009-02-26

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

Diff between micEcon versions 0.5-12 dated 2009-02-26 and 0.5-14 dated 2009-03-09

 DESCRIPTION                |    6 +++---
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Package ZIGP updated to version 3.3 with previous version 3.2 dated 2009-01-05

Author: Vinzenz Erhardt
Title: Zero Inflated Generalized Poisson (ZIGP) regression models
Description: Fit and analyze and compare GP, ZIP and ZIGP regression models

Diff between ZIGP versions 3.2 dated 2009-01-05 and 3.3 dated 2009-03-09

 DESCRIPTION         |    6 +-
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Package Rcsdp updated to version 0.1-3 with previous version 0.1-2 dated 2009-03-08

Author: Hector Corrada Bravo (CSDP by Brian Borchers)
Title: R interface to the CSDP semidefinite programming library
Description: R interface to the CSDP semidefinite programming library. Installs version 6.0.1 of CSDP from the COIN-OR website if required. An existing intallation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.

Diff between Rcsdp versions 0.1-2 dated 2009-03-08 and 0.1-3 dated 2009-03-09

 DESCRIPTION      |    6 +++---
 src/Makevars.in  |    6 +-----
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Package vcd updated to version 1.2-3 with previous version 1.2-2 dated 2009-02-05

Author: David Meyer, Achim Zeileis, Kurt Hornik
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was inspired by the book "Visualizing Categorical Data" by Michael Friendly.

Diff between vcd versions 1.2-2 dated 2009-02-05 and 1.2-3 dated 2009-03-09

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 vcd-1.2-3/vcd/NEWS                           |    4 ++++
 vcd-1.2-3/vcd/inst/NEWS                      |    4 ++++
 vcd-1.2-3/vcd/inst/doc/residual-shadings.pdf |   26 +++++++++++++-------------
 vcd-1.2-3/vcd/inst/doc/strucplot.pdf         |binary
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Package bear updated to version 2.3.0 with previous version 2.2.0 dated 2009-02-12

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 2-treatment, 2-sequence, 1-period parallel ABE study (2x2x1).

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Package SNPassoc updated to version 1.5-8 with previous version 1.5-7 dated 2009-03-04

Author: Juan R Gonzlez, Llus Armengol, Elisabet Guin, Xavier Sol, and Vctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.

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Package tlnise updated to version 1.0 with previous version 0.2-7 dated 2008-03-26

Author: S-PLUS original by Phil Everson; R port by Roger D. Peng
Title: Two-level normal independent sampling estimation
Description: Functions for two level normal models as described in Everson and Morris (2000). J. R. Statist. Soc. B, 62 prt 2, pp.399--412.

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Package sdcMicro updated to version 2.5.8 with previous version 2.5.7 dated 2009-02-10

Author: Matthias Templ, Berhard Meindl
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.

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Package pmml updated to version 1.2.10 with previous version 1.2.9 dated 2009-03-06

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.

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Package gogarch updated to version 0.6-8 with previous version 0.6-7 dated 2009-02-24

Author: Bernhard Pfaff
Title: Generalized Orthogonal GARCH (GO-GARCH) models
Description: Implementation of the GO-GARCH model class

Diff between gogarch versions 0.6-7 dated 2009-02-24 and 0.6-8 dated 2009-03-09

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Package gmm updated to version 1.0-3 with previous version 1.0-2 dated 2009-03-05

Author: Pierre Chausse
Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).

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Sun, 08 Mar 2009

Package mlegp updated to version 2.2.6 with previous version 2.2.5 dated 2008-12-21

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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Package rsm updated to version 1.11 with previous version 1.10 dated 2008-12-31

Author: Russell V. Lenth
Title: Response-surface analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make contour plots, obtain the path of steepest ascent, and do canonical analysis.

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Package randomLCA updated to version 0.6-2 with previous version 0.6-1 dated 2008-11-09

Author: Ken Beath
Title: Random Effects Latent Class Analysis
Description: Fits random effects latent class models, as well as standard latent class models.

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Package plm updated to version 1.1-1 with previous version 1.1-0 dated 2009-02-25

Author: Yves Croissant , Giovanni Millo
Title: Linear models for panel data
Description: A set of estimators and tests for panel data

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Package mclust02 updated to version 2.1-18 with previous version 2.1-17 dated 2008-05-16

Author: C. Fraley and A.E. Raftery, Dept. of Statistics, University of Washington. R port by Ron Wehrens.
Title: Model-based cluster analysis (older version)
Description: Model-based cluster analysis: the 2002 version of MCLUST

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Package mclust updated to version 3.1-10.3 with previous version 3.1-10 dated 2008-11-30

Author: Chris Fraley and Adrian Raftery
Title: Model-Based Clustering / Normal Mixture Modeling
Description: Model-based clustering and normal mixture modeling including Bayesian regularization

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Package introgress updated to version 1.1 with previous version 1.0 dated 2009-02-25

Author: Zachariah Gompert, C. Alex Buerkle
Title: introgress
Description: introgress provides functions for analyzing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. Functions are also provided for maximum likelihood estimation of molecular hybrid index and graphical analysis.

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Package ergm updated to version 2.2-1 with previous version 2.2-0 dated 2009-03-01

Author: Mark S. Handcock , David R. Hunter , Carter T. Butts , Steven M. Goodreau , Pavel N. Krivitsky , Martina Morris
Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis. For a list of functions type: help(package='ergm')

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Package codetools updated to version 0.2-2 with previous version 0.2-1 dated 2008-04-02

Author: Luke Tierney
Title: Code Analysis Tools for R
Description: Code analysis tools for R

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Package WhatIf updated to version 1.5-5 with previous version 1.5-4 dated 2007-10-14

Author: Heather Stoll , Gary King , Langche Zeng ,
Title: WhatIf: Software for Evaluating Counterfactuals
Description: Inferences about counterfactuals are essential for prediction, answering what if questions, and estimating causal effects. However, when the counterfactuals posed are too far from the data at hand, conclusions drawn from well-specified statistical analyses become based largely on speculation hidden in convenient modeling assumptions that few would be willing to defend. Unfortunately, standard statistical approaches assume the veracity of the model rather than revealing the degree of model-dependence, which makes this problem hard to detect. WhatIf offers easy-to-apply methods to evaluate counterfactuals that do not require sensitivity testing over specified classes of models. If an analysis fails the tests offered here, then we know that substantive inferences will be sensitive to at least some modeling choices that are not based on empirical evidence, no matter what method of inference one chooses to use. WhatIf implements the methods for evaluating counterfactuals discussed in Gary King and Langche Zeng, 2006, "The Dangers of Extreme Counterfactuals," Political Analysis 14 (2); and Gary King and Langche Zeng, 2007, "When Can History Be Our Guide? The Pitfalls of Counterfactual Inference," International Studies Quarterly 51 (March).

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New package TRIANG with initial version 1.0
Package: TRIANG
Type: Package
Title: Discrete triangular distributions
Version: 1.0
Date: 2009-02-19
Author: Tristan Senga Kiess\'{e}, Silvio S. Zocchi, C\'{e}lestin C. Kokonendji
Maintainer: Tristan Senga Kiess\'{e}
Description: This is a package for discrete triangular distributions which complete the classical discrete distributions like binomial, Poisson and Negative binomial.
License: GPL-2
Packaged: Fri Mar 6 18:46:11 2009; root

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Package R2jags updated to version 0.01-18 with previous version 0.01-17 dated 2009-03-05

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

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New package Rcsdp with initial version 0.1-2
Package: Rcsdp
Version: 0.1-2
Title: R interface to the CSDP semidefinite programming library
Author: Hector Corrada Bravo (CSDP by Brian Borchers)
Maintainer: Hector Corrada Bravo
Description: R interface to the CSDP semidefinite programming library. Installs version 6.0.1 of CSDP from the COIN-OR website if required. An existing intallation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.
LazyLoad: yes
Suggests: Matrix
Enhances: Matrix
License: file LICENSE
URL: https://projects.coin-or.org/Csdp/
Revision: 11
Packaged: Fri Mar 6 04:59:35 2009; rforge

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Package PBSmodelling updated to version 2.06 with previous version 2.01 dated 2008-10-26

Author: Jon T. Schnute , Alex Couture-Beil , Rowan Haigh , and Anisa Egeli
Title: PBS Modelling 2.06
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.

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Package AER updated to version 1.1-1 with previous version 1.1-0 dated 2009-02-05

Author: Christian Kleiber, Achim Zeileis
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette for a package overview.)

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More information about AER at CRAN
Permanent link

Fri, 06 Mar 2009

Package XML updated to version 2.3-0 with previous version 2.1-0 dated 2009-02-19

Author: Duncan Temple Lang (duncan@wald.ucdavis.edu)
Title: Tools for parsing and generating XML within R and S-Plus.
Description: This package provides many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".

Diff between XML versions 2.1-0 dated 2009-02-19 and 2.3-0 dated 2009-03-06

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Package MasterBayes updated to version 2.42 with previous version 2.41 dated 2008-12-04

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 2.41 dated 2008-12-04 and 2.42 dated 2009-03-06

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New package sdtoolkit with initial version 2.22
Package: sdtoolkit
Type: Package
Title: Scenario Discovery Tools to Support Robust Decision Making
Version: 2.22
Date: 2009-03-04
Author: Benjamin P. Bryant
Maintainer: Benjamin P. Bryant
Description: Implements algorithms to help with scenario discovery - currently only modified version of the the Patient Rule Induction Method.
License: GPL-3
Copyright: Code copyright held by Evolving Logic. Documentation copyright held by the RAND Corporation.
Packaged: Fri Mar 6 08:55:52 2009; bryant

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Package robCompositions updated to version 1.2 with previous version 1.0.1 dated 2009-01-20

Author: Matthias Templ, Karel Hron, Peter Filzmoser
Title: Robust Estimation for Compositional Data.
Description: This first version of the package includes methods for imputation of compositional data including robust methods. The package will be enhanced with other multivariate methods for compositional data in near future.

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Package rjags updated to version 1.0.3-7 with previous version 1.0.3-6 dated 2009-03-06

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

Diff between rjags versions 1.0.3-6 dated 2009-03-06 and 1.0.3-7 dated 2009-03-06

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Package pmml updated to version 1.2.9 with previous version 1.2.8 dated 2009-03-03

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 1.2.8 dated 2009-03-03 and 1.2.9 dated 2009-03-06

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Package pcalg updated to version 0.1-8 with previous version 0.1-7 dated 2008-04-16

Author: Markus Kalisch, Martin Maechler
Title: Estimating the skeleton and equivalence class of a DAG
Description: Standard and robust estimation of the skeleton (ugraph) and the equivalence class of a Directed Acyclic Graph (DAG) via the PC-Algorithm. The equivalence class is represented by its (unique) Completetd Partially Directed Acyclic Graph (CPDAG). The function pcSelect implements variable selection techniques. beta.special computes the "causal" effect (see Description).

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Package eRm updated to version 0.10-2 with previous version 0.10-1 dated 2008-07-20

Author: Patrick Mair, Reinhold Hatzinger
Title: Extended Rasch Modeling.
Description: eRm fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices. An eRm platform is provided at R-forge (see URL).

Diff between eRm versions 0.10-1 dated 2008-07-20 and 0.10-2 dated 2009-03-06

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Package MCMCglmm updated to version 1.05 with previous version 1.04 dated 2009-03-03

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

Diff between MCMCglmm versions 1.04 dated 2009-03-03 and 1.05 dated 2009-03-06

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Package DiagnosisMed updated to version 0.1.2.1 with previous version 0.1.2 dated 2008-10-15

Author: Pedro Brasil
Title: Diagnostic test accuracy evaluation for medical professionals.
Description: DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is - or soon will be - able to estimate sample size for common situations in diagnostic test accuracy, estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different analysis strategies into measures commonly used by health professionals.

Diff between DiagnosisMed versions 0.1.2 dated 2008-10-15 and 0.1.2.1 dated 2009-03-06

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Package tossm updated to version 1.2 with previous version 1.1 dated 2009-01-05

Author: Mark Bravington, Karen Martien, Dave Gregovich
Title: Testing of Spatial Structure Methods
Description: Provides a framework under which methods of detecting and managing genetic spatial structure in populations can be tested.

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Package mi updated to version 0.04-2 with previous version 0.02-03 dated 2009-01-07

Author: Andrew Gelman , Jennifer Hill , Masanao Yajima , Yu-Sung Su , Maria Grazia Pittau
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking

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Package gss updated to version 1.0-4 with previous version 1.0-3 dated 2009-03-04

Author: Chong Gu
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.

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New package ccems with initial version 1.0
Package: ccems
Type: Package
Title: Combinatorially Complex Equilibrium Model Selection
Version: 1.0
Date: 2008-12-29
Author: Tom Radivoyevitch
Maintainer: Tom Radivoyevitch
Description: Dissociation constants of quasi-equilibriums of enzymes and protein-ligand binding equilibriums in general are systematically scanned though possibilities of being infinity and/or equal to others. The automatically generated space of models is then fitted to data.
Depends: odesolve,snow
Imports:
Suggests: nws
Enhances:
License: GPL-2
LazyLoad: yes
LazyData: yes
URL: http://epbi-radivot.cwru.edu/ccems
Packaged: Thu Mar 5 17:49:48 2009; radivot

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Package surveillance updated to version 1.0-2 with previous version 0.9-9 dated 2008-01-21

Author: M. Hhle with contributions from T. Correa, M. Hofmann, C. Lang, M. Paul, A. Riebler and V. Wimmer
Title: Outbreak detection algorithms for surveillance data
Description: A package implementing statistical methods for the surveillance of infectious diseases. This boils down to modelling and outbreak detection of univariate and multivariate time series of counts resulting from routinely collected public health surveillance data. Currently the package contains an implementation of the typically outbreak detection procedures such as Stroup et. al (1989), Farrington et. al (1996), Rossi et al (1999), Rogerson and Yamada (2001), a Bayesian approach and a detector based on generalized likelihood ratios (GLR). Furthermore, inference methods for the infectious disease model in Held et al (2005) are provided. The package contains several real-world datasets and the ability to simulate outbreak data.

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Package rjags updated to version 1.0.3-6 with previous version 1.0.3-5 dated 2009-02-23

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

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Package memisc updated to version 0.95-17 with previous version 0.95-16 dated 2009-02-19

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.

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Package bio.infer updated to version 1.2-3 with previous version 1.2-2 dated 2009-02-19

Author: Lester L. Yuan
Title: Compute biological inferences
Description: Imports benthic count data, reformats this data, and computes environmental inferences from this data.

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New package SGCS with initial version 0.9
Package: SGCS
Type: Package
Title: Spatial Graph based Clustering Summaries for spatial point patterns
Version: 0.9
Date: 2009-03-05
Author: Tuomas Rajala
Maintainer: Tuomas Rajala
Depends: spatstat
Description: Graph based clustering summaries for spatial point patterns. Includes 3 functions: Connectivity function, Cumulative connectivity function and clustering function. All three are introduced in my Article 1.
License: GPL (>=2)
Packaged: Thu Mar 5 15:07:09 2009; tarajala

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Thu, 05 Mar 2009

Package sendplot updated to version 3.0.2 with previous version 3.0.0 dated 2009-03-03

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

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Package rrcov updated to version 0.5-01 with previous version 0.4-08 dated 2009-01-16

Author: Valentin Todorov
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point.

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New package rngwell19937 with initial version 0.5-0
Package: rngwell19937
Title: WELL19937a random number generator
Version: 0.5-0
Date: 2009-03-05
Author: Petr Savicky
Maintainer: Petr Savicky
Description: generator WELL19937a by F. Panneton, P. L'Ecuyer and M. Matsumoto with initialization using MRG32k5a by P. L'Ecuyer
License: file LICENSE
Packaged: Thu Mar 5 06:30:02 2009; petr

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Package gmm updated to version 1.0-2 with previous version 1.0-1 dated 2009-02-04

Author: Pierre Chausse
Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).

Diff between gmm versions 1.0-1 dated 2009-02-04 and 1.0-2 dated 2009-03-05

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Package anacor updated to version 0.9-8 with previous version 0.9-4 dated 2008-10-12

Author: Jan de Leeuw, Patrick Mair
Title: Simple and Canonical Correspondence Analysis.
Description: This package performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.

Diff between anacor versions 0.9-4 dated 2008-10-12 and 0.9-8 dated 2009-03-05

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Package R2jags updated to version 0.01-17 with previous version 0.01-16 dated 2009-02-23

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 0.01-16 dated 2009-02-23 and 0.01-17 dated 2009-03-05

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Package OAIHarvester updated to version 0.0-2 with previous version 0.0-1 dated 2009-03-03

Author: Kurt Hornik
Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0.

Diff between OAIHarvester versions 0.0-1 dated 2009-03-03 and 0.0-2 dated 2009-03-05

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Package MBA updated to version 0.0-5 with previous version 0.0-4 dated 2008-03-21

Author: Andrew O. Finley , Sudipto Banerjee
Title: Multilevel B-spline Approximation
Description: Scattered data interpolation with Multilevel B-Splines

Diff between MBA versions 0.0-4 dated 2008-03-21 and 0.0-5 dated 2009-03-05

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Package DTK updated to version 2.1 with previous version 1.1 dated 2009-03-03

Author: Matthew K. Lau
Title: Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes
Description: Functions for conducting and plotting Dunnett's modified Tukey-Kramer pairwise multiple comparison test accounting for unequal variance and unequal sample sizes.

Diff between DTK versions 1.1 dated 2009-03-03 and 2.1 dated 2009-03-05

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Wed, 04 Mar 2009

Package rattle updated to version 2.4.41 with previous version 2.4.40 dated 2009-03-03

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 2.4.40 dated 2009-03-03 and 2.4.41 dated 2009-03-04

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New package tslars with initial version 1.0
Package: tslars
Type: Package
Title: Least angle regression for time series analysis
Version: 1.0
Date: 2009-01-03
Author: Sarah Gelper
Maintainer: Sarah Gelper
Description: This package will help you to carry out a time series LARS analysis.
License: GPL
LazyLoad: yes
Packaged: Wed Mar 4 12:38:03 2009; sarah

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Package modehunt updated to version 1.0.4 with previous version 1.0.3 dated 2008-08-25

Author: Kaspar Rufibach and Guenther Walther
Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations X(1), ..., X(n) from a density f, this package provides five methods to perform a multiscale analysis about f as well as the necessary critical values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive correction term Gamma in either method offers another two approaches which are more powerful on small scales and less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically equivalent to the first and was introduced in Rufibach and Walther (2007).

Diff between modehunt versions 1.0.3 dated 2008-08-25 and 1.0.4 dated 2009-03-04

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Package RJaCGH updated to version 2.0.0 with previous version 1.5.7 dated 2008-10-22

Author: Oscar Rueda and Ramon Diaz-Uriarte . zlib from Jean-loup Gailly and Mark Adler; see README. Function "getHostname.System" from package R.utils by Henrik Bengtsson.
Title: Reversible Jump MCMC for the analysis of CGH arrays.
Description: Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. The selection of the number of states is made via their posterior probability computed by Reversible Jump Markov Chain Monte Carlo Methods. Also returns probabilistic common regions for gains/losses.

Diff between RJaCGH versions 1.5.7 dated 2008-10-22 and 2.0.0 dated 2009-03-04

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Package MCPMod updated to version 1.0-2 with previous version 1.0-1 dated 2009-02-13

Author: Bjoern Bornkamp, Jose Pinheiro and Frank Bretz
Title: Design and Analysis of Dose-Finding Studies
Description: This package implements a methodology for the design and analysis of dose-response studies that combines aspects of multiple comparison procedures and modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748). The package provides tools for the analysis of dose finding trials as well as a variety of tools necessary to plan a trial to be conducted with the MCPMod methodology.

Diff between MCPMod versions 1.0-1 dated 2009-02-13 and 1.0-2 dated 2009-03-04

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Package logcondens updated to version 1.3.3 with previous version 1.3.2 dated 2008-07-16

Author: Kaspar Rufibach and Lutz Duembgen
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), this package allows to compute a concave, piecewise linear function phi on [X(1), X(n)] with knots only in {X(1), X(2), ..., X(n)} such that L(phi) = sum_{i=1}^n W(i)*phi(X(i)) - int_{X(1)}^{X(n)} exp(phi(x)) dx is maximal, for some weights W(1), ..., W(n) s.t. sum_{i=1}^n W(i) = 1. According to the results in Duembgen and Rufibach (2009), this function phi maximizes the ordinary log-likelihood sum_{i=1}^n W(i)*phi(X(i)) under the constraint that phi is concave. The corresponding function exp(phi) is a log-concave probability density. Two algorithms are offered: An active set algorithm and one based on the pool-adjacent-violaters algorithm.

Diff between logcondens versions 1.3.2 dated 2008-07-16 and 1.3.3 dated 2009-03-04

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Package PhViD updated to version 1.0.1 with previous version 1.0 dated 2009-03-03

Author: Ismail Ahmed & Antoine Poncet
Title: Pharmacovigilance signal detection methods extended to the multiple comparison setting.
Description: PhViD proposes the main pharmacovigilance signal detection methods extended to the multiple comparison setting. Those functions can be used as standard R functions or through an user friendly interface (PhViD.gui)

Diff between PhViD versions 1.0 dated 2009-03-03 and 1.0.1 dated 2009-03-04

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New package tlemix with initial version 0.0.4
Package: tlemix
Type: Package
Title: Trimmed Maximum Likelihood Estimation
Version: 0.0.4
Date: 2009-02-19
Author: P. Neytchev, P. Filzmoser, R. Patnaik, A. Eisl and R. Boubela
Depends: flexmix
Imports: methods, flexmix, modeltools, stats4
Suggests: mvtnorm, flexmix, tcltk
Maintainer: Peter Filzmoser
Description: TLE implements a general framework for robust fitting of finite mixture models. Parameter estimation is performed using the EM algorithm.
License: GPL
LazyLoad: yes
Packaged: Tue Mar 3 12:15:13 2009; root

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Package rgrs updated to version 0.2-8 with previous version 0.2-6 dated 2009-02-25

Author: Julien Barnier
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.

Diff between rgrs versions 0.2-6 dated 2009-02-25 and 0.2-8 dated 2009-03-04

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Package reporttools updated to version 1.0.2 with previous version 1.0.1 dated 2008-11-13

Author: Kaspar Rufibach
Title: Generate LaTeX tables of descriptive statistics
Description: The functions in this package are especially helpful when writing reports of data analysis using Sweave.

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Package pspearman updated to version 0.1-10 with previous version 0.1-9 dated 2009-02-11

Author: Petr Savicky
Title: Spearman's rank correlation test
Description: Spearman's rank correlation test with improved accuracy

Diff between pspearman versions 0.1-9 dated 2009-02-11 and 0.1-10 dated 2009-03-04

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Package gss updated to version 1.0-3 with previous version 1.0-2 dated 2008-09-07

Author: Chong Gu
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.

Diff between gss versions 1.0-2 dated 2008-09-07 and 1.0-3 dated 2009-03-04

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Package compositions updated to version 1.01-1 with previous version 0.91-6 dated 2007-04-13

Author: K. Gerald van den Boogaart , Raimon Tolosana, Matevz Bren
Title: Compositional Data Analysis
Description: The package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by Aitchison and Pawlowsky-Glahn.

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Package clim.pact updated to version 2.2-30 with previous version 2.2-29 dated 2009-02-04

Author: Rasmus E. Benestad
Title: Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.
Description: The package contains R functions for retrieving data, making climate analysis and downscaling of monthly mean and daily mean global climate scenarios. (Windows-users may need to obtain the 'ncdf' package from URL 'http://www.stats.ox.ac.uk/pub/RWin/' to get clim.pact to work). The package is also described in the book 'Empirical-Statistical Downscaling (http://www.worldscibooks.com/environsci/6908.html)

Diff between clim.pact versions 2.2-29 dated 2009-02-04 and 2.2-30 dated 2009-03-04

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Package SNPassoc updated to version 1.5-7 with previous version 1.5-6 dated 2009-02-06

Author: Juan R Gonzlez, Llus Armengol, Elisabet Guin, Xavier Sol, and Vctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.

Diff between SNPassoc versions 1.5-6 dated 2009-02-06 and 1.5-7 dated 2009-03-04

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Package RQuantLib updated to version 0.2.11 with previous version 0.2.10 dated 2008-12-04

Author: Dirk Eddelbuettel
Title: R interface to the QuantLib library
Description: The RQuantLib package makes selected parts of QuantLib visible to the R user. Currently some basic option pricing functions are included, as well as fixed-income functions that can be used for interest rate curve construction and Bermuda swaption pricing. Further software contributions are welcome. The QuantLib project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets. The Windows binary version is self-contained and does not require a QuantLib (or Boost) installation. RQuantLib use the Rcpp R/C++ interface class library. See the Rcpp package on CRAN (or R-Forge) for more information on Rcpp. Note that while RQuantLib's code is licensed under the GPL (v2 or later), QuantLib itself is released under a somewhat less restrictive Open Source license (see QuantLib-License.txt).

Diff between RQuantLib versions 0.2.10 dated 2008-12-04 and 0.2.11 dated 2009-03-04

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New package BGSIMD with initial version 1.0
Package: BGSIMD
Type: Package
Title: Block Gibbs Sampler with Incomplete Multinomial Distribution
Version: 1.0
Date: 2009-02-06
Author: Kwang Woo Ahn , Kung-Sik Chan
Maintainer: Kwang Woo Ahn
Description: Implement an efficient block Gibbs sampler with incomplete data from a multinomial distribution taking values from the k categories 1,2,...,k, where data are assumed to miss at random and each missing datum belongs to one and only one of m distinct non-empty proper subsets A1, A2,..., Am of 1,2,...,k and the k categories are labelled such that only consecutive A's may overlap.
License: GPL (>= 2)
Packaged: Tue Mar 3 14:29:43 2009; kwooahn

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Tue, 03 Mar 2009

Package varSelRF updated to version 0.7-1 with previous version 0.6-5 dated 2008-04-17

Author: Ramon Diaz-Uriarte
Title: Variable selection using random forests
Description: Variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree plots; for the selection of large, potentially highly-correlated variables). Main applications in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications). You can use rpvm instead of Rmpi if you want but I've only tested with Rmpi.

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Package ucminf updated to version 1.0-4 with previous version 1.0-3 dated 2009-02-24

Author: Hans Bruun Nielsen and Stig Bousgaard Mortensen
Title: General-purpose unconstrained non-linear optimization
Description: An algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of 'ucminf' is designed for easy interchange with 'optim'.

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Package sendplot updated to version 3.0.0 with previous version 2.1.2 dated 2009-01-26

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

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Package rattle updated to version 2.4.40 with previous version 2.4.0 dated 2009-01-04

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.

Diff between rattle versions 2.4.0 dated 2009-01-04 and 2.4.40 dated 2009-03-03

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Package pmml updated to version 1.2.8 with previous version 1.2.0 dated 2009-01-05

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.

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Package mgcv updated to version 1.5-0 with previous version 1.4-2 dated 2009-02-13

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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More information about mgcv at CRAN
Permanent link

Package meta updated to version 0.9-18 with previous version 0.9-17 dated 2009-01-29

Author: Guido Schwarzer
Title: Meta-Analysis
Description: Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.

Diff between meta versions 0.9-17 dated 2009-01-29 and 0.9-18 dated 2009-03-03

 DESCRIPTION    |    6 +++---
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More information about meta at CRAN
Permanent link

Package hwriter updated to version 1.1 with previous version 1.0 dated 2009-02-08

Author: Gregoire Pau
Title: HTML Writer - Outputs R objects in HTML format
Description: Easy-to-use and versatile functions to output R objects in HTML format

Diff between hwriter versions 1.0 dated 2009-02-08 and 1.1 dated 2009-03-03

 DESCRIPTION            |    4 ++--
 DONE                   |    3 +++
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Permanent link

Package gWidgetsRGtk2 updated to version 0.0-51 with previous version 0.0-50 dated 2009-02-13

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

Diff between gWidgetsRGtk2 versions 0.0-50 dated 2009-02-13 and 0.0-51 dated 2009-03-03

 ChangeLog       |    5 +++++
 DESCRIPTION     |    4 ++--
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More information about gWidgetsRGtk2 at CRAN
Permanent link

New package PhViD with initial version 1.0
Package: PhViD
Type: Package
Title: What the package does (short line)
Version: 1.0
Date: 2009-02-11
Author: Ismail Ahmed & Antoine Poncet
Maintainer: Ismail Ahmed
Depends: LBE, MCMCpack, tcltk
Description: PhViD proposes the main pharmacovigilance signal detection methods extended to the multiple comparison setting. Those functions can be used as standard R functions or through an user friendly interface (PhViD.gui)
License: GPL 2
Packaged: Tue Mar 3 11:52:40 2009; isma

More information about PhViD at CRAN
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Package MCMCglmm updated to version 1.04 with previous version 1.03 dated 2009-02-24

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

Diff between MCMCglmm versions 1.03 dated 2009-02-24 and 1.04 dated 2009-03-03

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New package sparseLDA with initial version 0.1-5
Package: sparseLDA
Version: 0.1-5
Date: 2009-02-28
Title: Sparse Discriminant Analysis
Author: Line Clemmensen , contributions by Max Kuhn
Maintainer: Line Clemmensen
Depends: lars, elasticnet, MASS, mda
Description: Performs sparse linear discriminant analysis for gaussians and mixture of gaussians models.
License: GPL (>= 2)
URL: http://www.imm.dtu.dk/~lhc, https://r-forge.r-project.org/projects/sparselda/
Revision: 8
Packaged: Mon Mar 2 05:29:02 2009; rforge

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Package spBayes updated to version 0.1-1 with previous version 0.1-0 dated 2008-06-09

Author: Andrew O. Finley , Sudipto Banerjee , Bradley P. Carlin
Title: Univariate and Multivariate Spatial Modeling
Description: spBayes fits univariate and multivariate models with Markov chain Monte Carlo (MCMC).

Diff between spBayes versions 0.1-0 dated 2008-06-09 and 0.1-1 dated 2009-03-03

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More information about spBayes at CRAN
Permanent link

Package oce updated to version 0.1-76 with previous version 0.1-75 dated 2009-01-07

Author: Dan Kelley
Title: Analysis of Oceanographic data
Description: Supports the analysis of Oceanographic data, including CTD measurements, sea-level timeseries, coastline files, etc. Also includes functions for calculating seawater properties such as density, and derived properties such as buoyancy frequency.

Diff between oce versions 0.1-75 dated 2009-01-07 and 0.1-76 dated 2009-03-03

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More information about oce at CRAN
Permanent link

Package gWidgetsWWW updated to version 0.0-6 with previous version 0.0-5 dated 2009-02-10

Author: John Verzani
Title: Toolkit implementation of gWidgets for www
Description: Port of gWidgets API to www using Rpad to link R with a web page and Ext to create widgets. Processing code from http://ejohn.org/blog/processingjs

Diff between gWidgetsWWW versions 0.0-5 dated 2009-02-10 and 0.0-6 dated 2009-03-03

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New package lmomRFA with initial version 1.0
Package: lmomRFA
Version: 1.0
Date: 2009-03-01
Title: Regional frequency analysis using L-moments
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
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".
Depends: lmom
License: Common Public License Version 1.0
Packaged: Mon Mar 2 10:18:24 2009; hosking

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Package Ryacas updated to version 0.2-9 with previous version 0.2-7 dated 2007-09-09

Author: Rob Goedman , Gabor Grothendieck , Sren Hjsgaard , Ayal Pinkus
Title: R interface to the yacas computer algebra system
Description: An interface to the yacas computer algebra system.

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New package OAIHarvester with initial version 0.0-1
Package: OAIHarvester
Version: 0.0-1
Date: 2009-02-27
Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0.
Author: Kurt Hornik
Maintainer: Kurt Hornik
License: GPL-2
Imports: XML
Packaged: Tue Mar 3 08:55:34 2009; hornik

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Package DTK updated to version 1.1 with previous version 1.0 dated 2009-02-27

Author: Matthew K. Lau
Title: Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes
Description: Functions for conducting and plotting Dunnett's modified Tukey-Kramer pairwise multiple comparison test accounting for unequal variance and unequal sample sizes.

Diff between DTK versions 1.0 dated 2009-02-27 and 1.1 dated 2009-03-03

 DESCRIPTION        |    8 ++++----
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Mon, 02 Mar 2009

Package spatstat updated to version 1.15-0 with previous version 1.14-10 dated 2009-02-03

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, B. Biggerstaff, R. Bivand, F. Bonneu, J.B. Chen, Y.C. Chin, 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, J. Mateu, P. McCullagh, X.C. Mi, J. Moller, L.S. Nielsen, E. Parilov, J. Picka, M. Reiter, B.D. Ripley, B. Rowlingson, J. Rudge, A. Sarkka, K. Schladitz, B.T. Scott, I.-M. Sintorn, M. Spiess, M. Stevenson, P. Surovy, B. Turlach, A. van Burgel, H. Wang 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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New package mhsmm with initial version 0.1.0
Package: mhsmm
Type: Package
Title: Parameter estimation and prediction for multiple hidden Markov and semi-Markov models
Version: 0.1.0
Date: 2009-01-21
Author: Jared O'Connell with minor contributions from Soren Hojsgaard
Maintainer: Soren Hojsgaard
Description: Parameter estimation and prediction for multiple hidden Markov and semi-Markov models. The times must be equidistant but missing values of the observables are allowed. The observables are allowed to be multivariate. It is possible to have multiple sequences of data. Estimation of the parameters of the models are made using EM--algorithms. Crucial parts of the code is written in C which makes estimation fast. Finally, the package is made so that the user is allow to specify own components of the model.
License: GPL (>= 2)
LazyLoad: yes
Depends: mvtnorm
Packaged: Mon Mar 2 09:23:09 2009; SHD

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Package ltm updated to version 0.9-0 with previous version 0.8-9 dated 2009-01-08

Author: Dimitris Rizopoulos
Title: Latent Trait Models under IRT
Description: Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.

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Package fda updated to version 2.1.1 with previous version 2.1.0 dated 2009-01-03

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. A manual that describes the use of these functions is available in this library. The library also contains a number of the data sets used in the book along with R code for the analyses that produced many of the figures in the book.

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Package Rcpp updated to version 0.6.4 with previous version 0.6.3 dated 2009-01-11

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++.

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New package BAS with initial version 0.1
Package: BAS
Version: 0.1
Date: 2009-2-27
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Author: Merlise Clyde with contributions from Michael Littman
Maintainer: Merlise Clyde
Depends: R (>= 2.6)
SUGGESTS: MASS
Description: Package for Bayesian Model Averaging in linear models using stochastic or deterministic sampling without replacement from posterior distributions. Prior distributions on coefficients are from Zellner's g-prior or mixtures of g-priors corresponding to the Zellner-Siow Cauchy Priors or the Liang et al hyper-g priors (to appear JASA 2008). Other model selection criterian include AIC and BIC. Sampling probabilities may be updated based on the sampled models.
License: GPL (>= 2)
URL: http://www.r-project.org, http://www.isds.duke.edu/~clyde/BAS
Packaged: Sun Mar 1 19:16:28 2009; clyde

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Sun, 01 Mar 2009

New package fpow with initial version 0.0-1
Package: fpow
Version: 0.0-1
Date: 2009-03-01
Title: Computing the noncentrality parameter of the noncentral F distribution
Author: Ali Baharev
Maintainer: Ali Baharev
Description: Returns the noncentrality parameter of the noncentral F ditribution if probability of type I and type II error, degrees of freedom of the numerator and the denominator are given. It may be useful for computing minimal detecable differences for general ANOVA models. This program is documented in the paper of A. Baharev, S. Kemeny, On the computation of the noncentral F and noncentral beta distribution; Statistics and Computing, 2008, 18 (3), 333-340. http://dx.doi.org/10.1007/s11222-008-9061-3 Preprint of this paper is available at http://reliablecomputing.eu/ncbeta.html
License: GPL-2
Depends: R (>= 2.8.0)
Packaged: Sun Mar 1 20:11:52 2009; ali

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Package ergm updated to version 2.2-0 with previous version 2.1 dated 2008-04-28

Author: Mark S. Handcock , David R. Hunter , Carter T. Butts , Steven M. Goodreau , Pavel N. Krivitsky , Martina Morris
Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis. For a list of functions type: help(package='ergm')

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 ergm-2.2-0/ergm/src/MCMC.c                     |   15 
 ergm-2.2-0/ergm/src/MCMC.h                     |   15 
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 ergm-2.2-0/ergm/src/MHproposals_bipartite.c    |   15 
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 ergm-2.2-0/ergm/src/MPLE.c                     |   19 
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 ergm-2.2-0/ergm/src/changestats.c              | 2007 +++++++++++++++++--------
 ergm-2.2-0/ergm/src/changestats.h              |   29 
 ergm-2.2-0/ergm/src/edgetree.c                 |   46 
 ergm-2.2-0/ergm/src/edgetree.h                 |   25 
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 ergm-2.2-0/ergm/src/model.c                    |   15 
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 140 files changed, 5352 insertions(+), 2123 deletions(-)

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Package bayesclust updated to version 2.1 with previous version 1.1 dated 2009-02-03

Author: Gopal, V. and Fuentes, C. and Casella, G.
Title: Tests/Searches for significant clusters in genetic data.
Description: Bayes Clustering Package

Diff between bayesclust versions 1.1 dated 2009-02-03 and 2.1 dated 2009-03-01

 DESCRIPTION               |    6 ++--
 R/cluster.optimal.R       |   68 ++++++++++++++++++++--------------------------
 R/cluster.test.R          |   11 +++----
 R/fdr.test.R              |   11 +++----
 R/nulldensity.R           |    4 --
 man/bayesclust-package.Rd |    2 -
 man/cluster.optimal.Rd    |    4 +-
 man/cluster.test.Rd       |    4 +-
 man/fdr.test.Rd           |    9 ++----
 man/nulldensity.Rd        |    8 ++---
 src/GroupMH.c             |   40 ++++-----------------------
 src/nullsum.c             |   19 +-----------
 12 files changed, 64 insertions(+), 122 deletions(-)

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Package rda updated to version 1.0.1 with previous version 1.0 dated 2006-02-14

Author: Yaqian Guo Trevor Hastie Robert Tibshirani
Title: Shrunken Centroids Regularized Discriminant Analysis
Description: Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.

Diff between rda versions 1.0 dated 2006-02-14 and 1.0.1 dated 2009-03-01

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

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Package mota updated to version 1.2.1 with previous version 1.2 dated 2007-09-07

Author: Stefan Hengl
Title: Mean Optimal Transformation Approach
Description: Detect nonlinear functional relations. This package was originally designed for the identifiability analysis of nonlinear dynamical models. However, the concept is very general and allows to detect groups of functionally related variables whenever there are multiple estimates for each variable, which can be written in matrix K. The essence of the algorithm is the calculation of mean optimal transformations estimated from bootstrap samples drawn from K.

Diff between mota versions 1.2 dated 2007-09-07 and 1.2.1 dated 2009-03-01

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

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Package clusterRepro updated to version 0.5-1.1 with previous version 0.5-1 dated 2006-02-22

Author: Amy Kapp and Rob Tibshirani
Title: Reproducibility of gene expression clusters
Description: A function for validating microarry clusters via reproducibility

Diff between clusterRepro versions 0.5-1 dated 2006-02-22 and 0.5-1.1 dated 2009-03-01

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

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Package arm updated to version 1.2-7 with previous version 1.2-6 dated 2009-02-28

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 1.2-6 dated 2009-02-28 and 1.2-7 dated 2009-03-01

 CHANGELOG   |    5 +++++
 DESCRIPTION |    7 +++----
 R/display.R |   24 +++++++++++++++++-------
 3 files changed, 25 insertions(+), 11 deletions(-)

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New package RSurvey with initial version 0.4.3
Package: RSurvey
Type: Package
Title: Analysis of Spatially Distributed Data
Version: 0.4.3
Date: 2009-02-28
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
Depends: R (>= 2.8.0), tcltk, rgl, MBA, gpclib, sp, mgcv, tripack
Description: This package is a processing program for spatially distributed data. The program is capable of error corrections and data visualization. A graphical user interface is provided.
License: GPL (>= 2)
URL: https://eng.ucmerced.edu/people/jfisher/software/rsurvey
Packaged: Sat Feb 28 20:49:33 2009; jfisher

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