Thu, 22 Dec 2011

New package riskRegression with initial version 0.0.5
Package: riskRegression
Type: Package
Title: Risk regression for survival analysis
Version: 0.0.5
Date: 2011-17-11
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Depends: R (>= 1.9.1), prodlim (>= 1.2.9), rms, pec (>= 2.1.2)
Suggests: survival (>= 2.36), cmprsk (>= 2.2.2)
Maintainer: Thomas Alexander Gerds
Description: Risk regression models for survival analysis with and without competing risks
License: GPL (>= 2)
Packaged: 2011-12-22 16:58:21 UTC; grb615
Repository: CRAN
Date/Publication: 2011-12-22 19:10:55

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Package pec updated to version 2.1.2 with previous version 2.1.1 dated 2011-12-15

Title: Prediction Error Curves for Survival Models
Description: Validation of predicted surival probabilities using inverse weighting and resampling.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds

Diff between pec versions 2.1.1 dated 2011-12-15 and 2.1.2 dated 2011-12-22

 DESCRIPTION              |    6 +++---
 MD5                      |   12 ++++++------
 R/baselineHazard.coxph.R |    3 ++-
 R/pecMethods.R           |    2 +-
 R/plotPredictEventProb.R |    3 +--
 R/predictEventProb.R     |    2 +-
 R/predictSurvProb.R      |    1 -
 7 files changed, 14 insertions(+), 15 deletions(-)

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Package cgdsr updated to version 1.1.19 with previous version 1.1.18 dated 2011-12-14

Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS).
Description: The package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen
Maintainer: Anders Jacobsen

Diff between cgdsr versions 1.1.18 dated 2011-12-14 and 1.1.19 dated 2011-12-22

 DESCRIPTION                     |    8 ++++----
 MD5                             |   20 ++++++++++----------
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 inst/doc/cgdsr-005.pdf          |binary
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 inst/doc/cgdsr.pdf              |binary
 man/cgdsr-getCaseLists.Rd       |    2 +-
 man/cgdsr-getGeneticProfiles.Rd |    2 +-
 11 files changed, 34 insertions(+), 34 deletions(-)

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New package deseasonalize with initial version 1.0
Package: deseasonalize
Type: Package
Title: Optimal deseasonalization for geophysical time series using AR fitting
Version: 1.0
Date: 2011-12-21
Author: A. I. McLeod
Maintainer:
Depends: R (>= 2.10),lattice, FitAR
Description: Deseasonalize daily or monthly time series.
LazyLoad: yes
LazyData: yes
Classification/ACM: G.4, I.5
Classification/MSC: 62H30
License: GPL (>= 2)
Packaged: 2011-12-22 18:05:28 UTC; Aim
Repository: CRAN
Date/Publication: 2011-12-22 19:10:52

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Package gmaps (with last version 0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2011-01-06 0.2
2009-12-16 0.1.1
2008-03-06 0.1

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Package subselect updated to version 0.11-3 with previous version 0.11-2 dated 2011-10-23

Title: Selecting variable subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira , Pedro Duarte Silva , Jorge Cadima , Manuel Minhoto
Maintainer: Jorge Cadima

Diff between subselect versions 0.11-2 dated 2011-10-23 and 0.11-3 dated 2011-12-22

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 MD5                    |   54 ++++++++++++++++++++++++-------------------------
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 R/validmat.R           |    2 -
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 src/MStcrt.cpp         |    6 +++--
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 src/VSQforms.cpp       |    2 -
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 src/Vsmabo.h           |    6 ++---
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 28 files changed, 137 insertions(+), 135 deletions(-)

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Package survAUC updated to version 1.0-4 with previous version 1.0-3 dated 2011-12-01

Title: Estimators of prediction accuracy for time-to-event data.
Description: The package provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
Author: Sergej Potapov, Werner Adler and Matthias Schmid.
Maintainer: Sergej Potapov

Diff between survAUC versions 1.0-3 dated 2011-12-01 and 1.0-4 dated 2011-12-22

 DESCRIPTION           |    6 +--
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 10 files changed, 113 insertions(+), 12 deletions(-)

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Package gWidgetsRGtk2 updated to version 0.0-78 with previous version 0.0-77 dated 2011-10-24

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

Diff between gWidgetsRGtk2 versions 0.0-77 dated 2011-10-24 and 0.0-78 dated 2011-12-22

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 NEWS            |    4 ++
 R/aaaGenerics.R |    8 ++--
 R/ggraphics.R   |   15 ++++++--
 R/gvarbrowser.R |  102 +++++++++++++++++++++++++++++++-------------------------
 TODO.txt        |    1 
 8 files changed, 99 insertions(+), 63 deletions(-)

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Package ctv updated to version 0.7-4 with previous version 0.7-3 dated 2011-07-27

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

Diff between ctv versions 0.7-3 dated 2011-07-27 and 0.7-4 dated 2011-12-22

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 inst/ctv/ChemPhys.ctv                  |   14 +
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 inst/ctv/Distributions.ctv             |   31 ++-
 inst/ctv/Econometrics.ctv              |   33 ++-
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 inst/ctv/ExperimentalDesign.ctv        |  234 +++++++++++++++++------
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 inst/ctv/HighPerformanceComputing.ctv  |   63 +++++-
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 inst/ctv/NaturalLanguageProcessing.ctv |  137 +++++++++----
 inst/ctv/OfficialStatistics.ctv        |   59 ++++--
 inst/ctv/Optimization.ctv              |   89 ++++++---
 inst/ctv/Phylogenetics.ctv             |  104 +++-------
 inst/ctv/Psychometrics.ctv             |   60 +++++-
 inst/ctv/ReproducibleResearch.ctv      |   27 +-
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 inst/ctv/Survival.ctv                  |   14 -
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 30 files changed, 1109 insertions(+), 554 deletions(-)

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Package RMAWGEN updated to version 1.2 with previous version 1.1 dated 2011-09-28

Title: RMAWGEN (R Multi-site Auto-regressive Weather GENeretor): a package to generate daily time series from monthly mean values
Description: This package contains S3 and S4 functions for spatial multi-site stochastic generation of daily timeseries of temperature and precipitation. The implemented tools make use of Vectorial AutoRegressive models (VARs). The VAR is calibrated by daily instrumental "Gaussinized" time series and then works with monthly timeseries as input. Bugs/comments/questions/collaboration of any kind are warmly welcomed.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano

Diff between RMAWGEN versions 1.1 dated 2011-09-28 and 1.2 dated 2011-12-22

 DESCRIPTION                                           |   53 ++-
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 man/extractTxFromAnomalies.Rd                         |   36 ++
 man/extractdays.Rd                                    |   51 ++-
 man/extractmonths.Rd                                  |   54 ++-
 man/extractyears.Rd                                   |   50 ++-
 man/findDate.Rd                                       |   62 +++-
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 man/forecastResidual.Rd                               |   39 ++
 man/generateTemperatureTimeseries.Rd                  |  148 +++++++---
 man/getDailyMean.Rd                                   |   63 +++-
 man/getMonthlyMean.Rd                                 |   65 +++-
 man/getVARmodel.Rd                                    |  104 +++++--
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 120 files changed, 2479 insertions(+), 942 deletions(-)

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Package mosaic updated to version 0.2-3 with previous version 0.1-51 dated 2011-09-08

Title: Project MOSAIC (mosaic-web.org) math and stats teaching utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is creating a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim , Daniel Kaplan , Nicholas Horton
Maintainer: Randall Pruim

Diff between mosaic versions 0.1-51 dated 2011-09-08 and 0.2-3 dated 2011-12-22

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Package mixcat updated to version 1.0-1 with previous version 1.0-0 dated 2011-09-14

Title: Mixed effects cumulative link and logistic regression models
Description: Mixed effects cumulative and baseline logit link models for the analysis of ordinal or nominal responses, with non-parametric distribution for the random effects
Author: Georgios Papageorgiou and John Hinde
Maintainer: Georgios Papageorgiou

Diff between mixcat versions 1.0-0 dated 2011-09-14 and 1.0-1 dated 2011-12-22

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Package libamtrack updated to version 0.5.2 with previous version 0.5.1 dated 2011-08-05

Title: Computational routines for proton and ion radiotherapy
Description: This package is the R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R autoconversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich

Diff between libamtrack versions 0.5.1 dated 2011-08-05 and 0.5.2 dated 2011-12-22

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Package indicspecies updated to version 1.6.0 with previous version 1.5.2 dated 2011-06-29

Title: Functions to assess the strength and significance of relationship of species site group associations
Description: This package provides a set of functions to assess the strength of species site group associations. It is also possible to check the statistical significance of such associations.
Author: Miquel De Caceres, Florian Jansen
Maintainer: Miquel De Caceres

Diff between indicspecies versions 1.5.2 dated 2011-06-29 and 1.6.0 dated 2011-12-22

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Package forecast updated to version 3.15 with previous version 3.14 dated 2011-12-09

Title: Forecasting functions for time series
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman with contributions from Slava Razbash
Maintainer: Rob J Hyndman

Diff between forecast versions 3.14 dated 2011-12-09 and 3.15 dated 2011-12-22

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Package adabag updated to version 3.0 with previous version 2.1 dated 2011-10-23

Title: Applies AdaBoost.M1, AdaBoost-SAMME and Bagging
Description: This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation predictions can be done. Since version 2.0 a new function "margins" is available to calculate the margins for these classifiers. Also a higher flexibility is achieved giving access to the "rpart.control" argument of "rpart". Four important new features have been introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is implemented and a new function "errorevol" shows the error of the ensembles as a function of the number of iterations. In addition, the ensembles can be pruned using the option "newmfinal" in the predict.bagging and predict.boosting functions and the posterior probability of each class for observations can be obtained.
Author: Alfaro-Cortes, Esteban; Gamez-Martinez, Matias and Garcia-Rubio, Noelia
Maintainer: Esteban Alfaro-Cortes

Diff between adabag versions 2.1 dated 2011-10-23 and 3.0 dated 2011-12-22

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Package topologyGSA updated to version 1.0.3 with previous version 1.0.2 dated 2011-11-10

Title: topologyGSA
Description: Package description.
Author: Sofia Massa, Gabriele Sales
Maintainer: Sofia Massa

Diff between topologyGSA versions 1.0.2 dated 2011-11-10 and 1.0.3 dated 2011-12-22

 DESCRIPTION |    6 +++---
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Package semPLS updated to version 1.0-5 with previous version 1.0-4 dated 2011-12-21

Title: Structural Equation Modeling Using Partial Least Squares
Description: Fits structural equation models using partial least squares (PLS). The PLS approach is referred to as 'soft-modeling' technique requiring no distributional assumptions on the observed data.
Author: Armin Monecke
Maintainer: Armin Monecke

Diff between semPLS versions 1.0-4 dated 2011-12-21 and 1.0-5 dated 2011-12-22

 DESCRIPTION      |    6 +++---
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Package R.utils updated to version 1.9.7 with previous version 1.9.6 dated 2011-11-24

Title: Various programming utilities
Description: This package provides utility classes and methods useful when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.utils versions 1.9.6 dated 2011-11-24 and 1.9.7 dated 2011-12-22

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Package Rcpp updated to version 0.9.8 with previous version 0.9.7 dated 2011-09-30

Title: Seamless R and C++ Integration
Description: The Rcpp package provides a C++ library which facilitates the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Several examples are included, and more than 750 unit tests in over 330 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development, however, should use the Rcpp package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois

Diff between Rcpp versions 0.9.7 dated 2011-09-30 and 0.9.8 dated 2011-12-22

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More information about Rcpp at CRAN
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Package RcmdrPlugin.BCA updated to version 0.9-1 with previous version 0.1-4 dated 2011-05-05

Title: Rcmdr Plug-In for Business and Customer Analytics
Description: This package provides an Rcmdr "plug-in" to accompany the book Customer and Business Analytics: Applied Data Mining for Business Decision Making Using R by Daniel S. Putler and Robert E. Krider.
Author: Dan Putler
Maintainer: Dan Putler

Diff between RcmdrPlugin.BCA versions 0.1-4 dated 2011-05-05 and 0.9-1 dated 2011-12-22

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Package raster updated to version 1.9-58 with previous version 1.9-55 dated 2011-12-11

Title: Geographic analysis and modeling with raster data
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions, as well as map algebra. Processing of very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans

Diff between raster versions 1.9-55 dated 2011-12-11 and 1.9-58 dated 2011-12-22

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New package R2admb with initial version 0.7.5
Package: R2admb
Type: Package
Title: ADMB to R interface functions
Version: 0.7.5
Date: 2012-12-18
Author: Ben Bolker, Hans Skaug
Maintainer: Ben Bolker
Description: A series of functions to call AD Model Builder (i.e., compile and run models) from within R, read the results back into R as "admb" objects, and provide standard accessors (i.e. coef(), vcov(), etc.)
Suggests: bbmle, lattice, coda, lme4, ggplot2
License: GPL
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: r2admb
Repository/R-Forge/Revision: 69
Date/Publication: 2011-12-22 08:26:04
Packaged: 2011-12-19 21:48:49 UTC; rforge

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Package paleoTS updated to version 0.4-2 with previous version 0.4-1 dated 2011-03-15

Title: Analyze paleontological time-series
Description: This package facilitates analysis of paleontological sequences of trait values from an evolving lineage. Functions are provided to fit, using maximum likelihood, evolutionary models including unbiased random walks, directional evolution, stasis, Ornstein-Uhlenbeck, punctuated change, and evolutionary models in which traits track some measured covariate.
Author: Gene Hunt
Maintainer: Gene Hunt

Diff between paleoTS versions 0.4-1 dated 2011-03-15 and 0.4-2 dated 2011-12-22

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 paleoTS-0.4-2/paleoTS/man/LRI.Rd             |    6 +++---
 paleoTS-0.4-2/paleoTS/man/as.paleoTS.Rd      |   15 ++++++++++-----
 paleoTS-0.4-2/paleoTS/man/fit.sgs.Rd         |    4 ++--
 paleoTS-0.4-2/paleoTS/man/fit3models.Rd      |    2 +-
 paleoTS-0.4-2/paleoTS/man/fitGpunc.Rd        |    2 +-
 paleoTS-0.4-2/paleoTS/man/lynchD.Rd          |    4 ++--
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 paleoTS-0.4-2/paleoTS/man/paleoTS-package.Rd |    6 ++++--
 paleoTS-0.4-2/paleoTS/man/plot.paleoTS.Rd    |   14 ++++++++------
 paleoTS-0.4-2/paleoTS/man/sim.OU.Rd          |    2 +-
 paleoTS-0.4-2/paleoTS/man/stickleback.Rd     |    7 +++++--
 paleoTS-0.4-2/paleoTS/man/sub.paleoTS.Rd     |    2 +-
 18 files changed, 43 insertions(+), 36 deletions(-)

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Package maxent updated to version 1.3.1 with previous version 1.3.0 dated 2011-12-05

Title: Low-memory Multinomial Logistic Regression with Support for Text Classification
Description: maxent is an R package with tools for low-memory multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm package.
Author: Timothy P. Jurka
Maintainer: Timothy P. Jurka

Diff between maxent versions 1.3.0 dated 2011-12-05 and 1.3.1 dated 2011-12-22

 ChangeLog                   |   12 +++++++++---
 DESCRIPTION                 |    8 ++++----
 MD5                         |   20 ++++++++++----------
 man/as.compressed.matrix.Rd |    2 ++
 man/load.model.Rd           |    9 +++------
 man/maxent-class.Rd         |    2 ++
 man/maxent-package.Rd       |   10 ++++------
 man/maxent.Rd               |   17 +++++++++++++++--
 man/predict.maxent.Rd       |    6 ++----
 man/save.model.Rd           |    2 ++
 man/tune.maxent.Rd          |   12 ++++++++++++
 11 files changed, 65 insertions(+), 35 deletions(-)

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Package informR updated to version 1.0.03 with previous version 1.0.01 dated 2011-08-30

Title: informR: R Tools for Creating Sequence Statistics
Description: Tools for creating sequence statistics, especially for Butts's egocentric relational event model fitting software in the relevent R package
Author: Christopher Steven Marcum
Maintainer: Christopher Steven Marcum

Diff between informR versions 1.0.01 dated 2011-08-30 and 1.0.03 dated 2011-12-22

 ChangeLog            |   10 ++++++++++
 DESCRIPTION          |   12 +++++-------
 MD5                  |   17 ++++++++++-------
 R/gen.sformlist.R    |   50 +++++++++++++++++++++++++++++++++++++++++++++-----
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 R/zzz.R              |   21 ++++-----------------
 man/gen.sformlist.Rd |   35 +++++++++++++++++++++++++++++++++--
 man/glb.sformlist.Rd |only
 man/sfl2sl.Rd        |   11 ++++++++++-
 11 files changed, 122 insertions(+), 43 deletions(-)

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Package GenSA updated to version 1.0.2 with previous version 1.0.1 dated 2011-11-29

Title: R functions for Generalized Simulated Annealing
Description: This package searches for global minimum of a very complex non-linear objective function with a very large number of optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian

Diff between GenSA versions 1.0.1 dated 2011-11-29 and 1.0.2 dated 2011-12-22

 DESCRIPTION    |    8 ++++----
 MD5            |   10 +++++-----
 NEWS           |    7 ++++---
 man/GenSA.Rd   |   27 +++++++++++++++++----------
 src/Caller.cpp |    2 +-
 src/Engine.cpp |    2 +-
 6 files changed, 32 insertions(+), 24 deletions(-)

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Package fastmatch updated to version 1.0-3 with previous version 1.0-2 dated 2011-09-14

Title: Fast match() function
Description: Package providing a fast match() replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match() function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between fastmatch versions 1.0-2 dated 2011-09-14 and 1.0-3 dated 2011-12-22

 DESCRIPTION     |   14 +++++++-------
 MD5             |    6 +++---
 NEWS            |    9 +++++++++
 src/fastmatch.c |   32 ++++++++++++++++++++++++--------
 4 files changed, 43 insertions(+), 18 deletions(-)

More information about fastmatch at CRAN
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Package dplR updated to version 1.5.1 with previous version 1.5.0 dated 2011-11-24

Title: Dendrochronology Program Library in R
Description: This package contains functions for performing tree-ring analyses, IO, and graphics.
Author: Andy Bunn with major additions from Mikko Korpela and other significant contributions from Franco Biondi and Christian Zang
Maintainer: Andy Bunn

Diff between dplR versions 1.5.0 dated 2011-11-24 and 1.5.1 dated 2011-12-22

 ChangeLog           |   17 +++++++
 DESCRIPTION         |   10 ++--
 MD5                 |   24 +++++------
 R/corr.rwl.seg.R    |  111 +++++++++++++++++++++++++++++++++++++++-------------
 R/corr.series.seg.R |    7 +--
 data/ca533.rda      |binary
 data/cana157.rda    |binary
 data/co021.rda      |binary
 data/gp.d2pith.rda  |binary
 data/gp.dbh.rda     |binary
 data/gp.po.rda      |binary
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 man/corr.rwl.seg.Rd |  109 +++++++++++++++++++++++++++++----------------------
 13 files changed, 186 insertions(+), 92 deletions(-)

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Package BCA updated to version 0.9-1 with previous version 0.1-1 dated 2011-05-05

Title: Business and Customer Analytics
Description: Underlying support functions for RcmdrPlugin.BCA and a companion to the book Customer and Business Analytics: Applied Data Mining for Business Decision Making Using R by Daniel S. Putler and Robert E. Krider
Author: Dan Putler
Maintainer: Dan Putler

Diff between BCA versions 0.1-1 dated 2011-05-05 and 0.9-1 dated 2011-12-22

 DESCRIPTION        |   18 +++----
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 NAMESPACE          |    3 +
 R/BCA.R            |  121 +++++++++++++++++++++++++++++++++++++++++++++++++----
 data/jack.jill.rda |only
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 8 files changed, 133 insertions(+), 24 deletions(-)

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