CRANberries

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

Sun, 14 Mar 2010

Package sem updated to version 0.9-20 with previous version 0.9-19 dated 2009-10-11

Title: Structural Equation Models
Description: This package contains functions for fitting general linear structural equation models (with observed and unobserved variables) by the method of maximum likelihood using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox with contributions from Adam Kramer and Michael Friendly
Maintainer: John Fox

Diff between sem versions 0.9-19 dated 2009-10-11 and 0.9-20 dated 2010-03-14

 DESCRIPTION  |   10 +++++-----
 R/sem.R      |    4 ++--
 inst/CHANGES |    4 ++++
 3 files changed, 11 insertions(+), 7 deletions(-)

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

Package R.oo updated to version 1.7.0 with previous version 1.6.7 dated 2010-01-22

Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.oo versions 1.6.7 dated 2010-01-22 and 1.7.0 dated 2010-03-14

 DESCRIPTION     |    8 ++++----
 NAMESPACE       |only
 R/999.package.R |    5 +++++
 R/zzz.R         |    4 +++-
 inst/NEWS       |    4 ++++
 5 files changed, 16 insertions(+), 5 deletions(-)

More information about R.oo at CRAN
Path: /cran/updated | permanent link

Package R.methodsS3 updated to version 1.2.0 with previous version 1.1.0 dated 2010-01-03

Title: Utility function for defining S3 methods
Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future want to migrate to S4. This is a cross-platform package implemented in pure R and generates standard S3 methods.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.methodsS3 versions 1.1.0 dated 2010-01-03 and 1.2.0 dated 2010-03-14

 DESCRIPTION |    8 ++++----
 NAMESPACE   |only
 R/zzz.R     |    4 +++-
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 4 files changed, 11 insertions(+), 5 deletions(-)

More information about R.methodsS3 at CRAN
Path: /cran/updated | permanent link

Package R.cache updated to version 0.3.0 with previous version 0.2.0 dated 2009-10-18

Title: Fast and light-weight caching of objects
Description: Methods for memoization, that is, caching arbitrary R objects in persistent memory. Objects can be loaded and saved stratified on a set of hashing objects.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.cache versions 0.2.0 dated 2009-10-18 and 0.3.0 dated 2010-03-14

 DESCRIPTION |   10 ++++------
 NAMESPACE   |only
 R/zzz.R     |    3 ++-
 inst/NEWS   |    4 ++++
 4 files changed, 10 insertions(+), 7 deletions(-)

More information about R.cache at CRAN
Path: /cran/updated | permanent link

Package RcmdrPlugin.MAd updated to version 0.2 with previous version 0.1 dated 2010-03-13

Title: Meta-Analysis with Mean Differences (MAd) Rcmdr Plug-in
Description: This is an R-Commander plug-in for the MAd package (Meta-Analysis with Mean Differences). This package enables the user to conduct a meta-analysis in a menu-driven, graphical user interface environment (e.g., SPSS), while having the full statistical capabilities of R and the MAd package. The MAd package itself contains a variety of useful functions for conducting a research synthesis with mean differences data. One of the unique features of the MAd package is in its integration of user-friendly functions to complete many of the statistical steps involved in a meta-analysis with mean differences. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re
Maintainer: AC Del Re

Diff between RcmdrPlugin.MAd versions 0.1 dated 2010-03-13 and 0.2 dated 2010-03-14

 DESCRIPTION                    |   12 ++++-----
 inst/etc/menus.txt             |   52 ++++++++++++++++++++---------------------
 man/RcmdrPlugin.MAd-package.Rd |   20 +++++++--------
 3 files changed, 42 insertions(+), 42 deletions(-)

More information about RcmdrPlugin.MAd at CRAN
Path: /cran/updated | permanent link

Package pcalg updated to version 1.0-0 with previous version 0.1-9 dated 2009-09-23

Title: Estimation of CPDAG/PAG and causal inference using the IDA algorithm
Description: Standard and robust estimation of 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). Furthermore, a PAG instead of a CPDAG can be estimated if latent variables and/or selection variables are assumed to be present. Functions for causal inference using the IDA algorithm (based on do-calculus of Judea Pearl) are provided for CPDAGs.
Author: Markus Kalisch, Martin Maechler, Diego Colombo
Maintainer: Markus Kalisch

Diff between pcalg versions 0.1-9 dated 2009-09-23 and 1.0-0 dated 2010-03-14

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 43 files changed, 1966 insertions(+), 344 deletions(-)

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

Package RcmdrPlugin.MAc updated to version 1.0.7 with previous version 1.0.6 dated 2010-03-13

Title: Meta-Analysis with Correlations (MAc) Rcmdr Plug-in
Description: This is an R-Commander plug-in for the MAc package (Meta-Analysis with Correlations). This package enables the user to conduct a meta-analysis in a menu-driven, graphical user interface environment (e.g., SPSS), while having the full statistical capabilities of R and the MAc package. The MAc package itself contains a variety of useful functions for conducting a research synthesis with correlational data. One of the unique features of the MAc package is in its integration of user-friendly functions to complete the majority of statistical steps involved in a meta-analysis with correlations. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re
Maintainer: AC Del Re

Diff between RcmdrPlugin.MAc versions 1.0.6 dated 2010-03-13 and 1.0.7 dated 2010-03-14

 DESCRIPTION                    |    8 ++---
 R/RcmdrPlugin.R                |    1 
 inst/etc/menus.txt             |   60 ++++++++++++++++++++---------------------
 man/RcmdrPlugin.MAc-package.Rd |   10 +++---
 4 files changed, 40 insertions(+), 39 deletions(-)

More information about RcmdrPlugin.MAc at CRAN
Path: /cran/updated | permanent link

Package RSurvey updated to version 0.5.0 with previous version 0.4.9 dated 2010-02-15

Title: Analysis of Spatially Distributed Data
Description: This package is a processing program for spatially distributed data. The program is capable of error corrections, polygon manipulation, and data visualization. A graphical user interface is provided.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher

Diff between RSurvey versions 0.4.9 dated 2010-02-15 and 0.5.0 dated 2010-03-14

 DESCRIPTION             |    8 +-
 R/polyAutocrop.R        |    3 
 R/polyManage.R          |  164 +++++++++++++++++++++++++-----------------------
 R/srvy.R                |    8 +-
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 R/srvy.vars.R           |    6 -
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 man/RSurvey-package.Rd  |   22 ++----
 man/autocrop.Rd         |    2 
 man/axesLimits.Rd       |   16 ++--
 man/getFile.Rd          |    2 
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 man/plotSurvey3d.Rd     |   10 +-
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 man/srvy.dat.Rd         |   18 ++---
 man/srvy.pref.Rd        |    2 
 25 files changed, 254 insertions(+), 222 deletions(-)

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

Sat, 13 Mar 2010

Package hergm updated to version 1.1-1 with previous version 1.1 dated 2010-03-11

Title: Hierarchical Exponential-Family Random Graph Models
Description: The R package 'hergm' implements Hierarchical Exponential-Family Random Graph Models (HERGMs), which can be used to model a wide range of relational data (networks). 'hergm' implements both simulation and Bayesian inference.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger

Diff between hergm versions 1.1 dated 2010-03-11 and 1.1-1 dated 2010-03-13

 hergm-1.1-1/hergm/DESCRIPTION              |    8 ++++----
 hergm-1.1-1/hergm/R/hergm.postprocess.R    |    9 +++++++--
 hergm-1.1-1/hergm/R/hergm.preprocess.R     |    3 ++-
 hergm-1.1-1/hergm/R/hergm.relabel.R        |    3 +--
 hergm-1.1-1/hergm/demo/example.r           |    3 ++-
 hergm-1.1-1/hergm/man/hergm.postprocess.Rd |    3 +++
 hergm-1.1-1/hergm/src/h_ergm.c             |    2 ++
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 8 files changed, 21 insertions(+), 10 deletions(-)

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

Package PwrGSD updated to version 1.16 with previous version 1.15 dated 2008-07-11

Title: Power in a Group Sequential Design
Description: Tools the evaluation of interim analysis plans for sequentially monitored trials on a survival endpoint; tools to construct efficacy and futility boundaries, for deriving power of a sequential design at a specified alternative, template for evaluating the performance of candidate plans at a set of time varying alternatives.
Author: Grant Izmirlian
Maintainer: Grant Izmirlian

Diff between PwrGSD versions 1.15 dated 2008-07-11 and 1.16 dated 2010-03-13

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 PwrGSD-1.16/PwrGSD/DESCRIPTION                                       |   13 
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 98 files changed, 1690 insertions(+), 1570 deletions(-)

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

Package tractor.base updated to version 1.4.0 with previous version 1.3.0 dated 2009-11-10

Title: Basic functions for the TractoR (tractography with R) bundle
Description: The tractor.base package consists of functions for working with magnetic resonance images. It can read and write image files stored in Analyze, NIfTI and DICOM formats (DICOM support is read only), generate images for use as regions of interest, and manipulate and visualise images.
Author: Jon Clayden
Maintainer: Jon Clayden

Diff between tractor.base versions 1.3.0 dated 2009-11-10 and 1.4.0 dated 2010-03-13

 DESCRIPTION                |    8 -
 R/dicom.R                  |  183 ++++++++++++++++++++++++++++++---------------
 R/generate.R               |    7 +
 R/misc.R                   |   12 ++
 R/mri_image.R              |   29 +++++++
 R/output.R                 |    5 -
 R/png.R                    |    2 
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 data/dictionary.txt        |    1 
 man/newMriImageWithData.Rd |    7 +
 man/output.Rd              |    2 
 man/visualisation.Rd       |    6 +
 12 files changed, 246 insertions(+), 74 deletions(-)

More information about tractor.base at CRAN
Path: /cran/updated | permanent link

Package seriation updated to version 1.0-2 with previous version 1.0-1 dated 2009-08-25

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.
Author: Michael Hahsler, Christian Buchta and Kurt Hornik
Maintainer: Michael Hahsler

Diff between seriation versions 1.0-1 dated 2009-08-25 and 1.0-2 dated 2010-03-13

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

Package samr updated to version 1.28 with previous version 1.27 dated 2010-01-04

Title: SAM: Significance Analysis of Microarrays
Description: Significance Analysis of Microarrays
Author: R. Tibshirani, G. Chu, T. Hastie, Balasubramanian Narasimhan
Maintainer: Rob Tibshirani

Diff between samr versions 1.27 dated 2010-01-04 and 1.28 dated 2010-03-13

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

Package nleqslv updated to version 1.6 with previous version 1.5 dated 2009-09-05

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.
Author: Berend Hasselman
Maintainer: Berend Hasselman

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

Package multtest updated to version 2.3.2 with previous version 2.2.0 dated 2009-11-13

Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Maintainer: Katherine S. Pollard

Diff between multtest versions 2.2.0 dated 2009-11-13 and 2.3.2 dated 2010-03-13

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

Package gsDesign updated to version 2.2-11 with previous version 2.0-5 dated 2009-07-01

Title: Group Sequential Design
Description: gsDesign is a package that derives group sequential designs and describes their properties.
Author: Keaven Anderson
Maintainer: Keaven Anderson

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

Package cocorresp updated to version 0.1-9 with previous version 0.1-7 dated 2008-10-23

Title: Co-correspondence analysis methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communitities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson. Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson

Diff between cocorresp versions 0.1-7 dated 2008-10-23 and 0.1-9 dated 2010-03-13

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

Package bayesclust updated to version 3.0 with previous version 2.1 dated 2009-03-01

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

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

Package analogue updated to version 0.6-23 with previous version 0.6-22 dated 2009-11-05

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.
Author: Gavin L. Simpson, Jari Oksanen
Maintainer: Gavin L. Simpson

Diff between analogue versions 0.6-22 dated 2009-11-05 and 0.6-23 dated 2010-03-13

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

Package TGUITeaching updated to version 0.9.6 with previous version 0.9.5 dated 2010-03-12

Title: Teaching GUI - prototype
Description: Trainings-GUI
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Maintainer: Bernhard Meindl

Diff between TGUITeaching versions 0.9.5 dated 2010-03-12 and 0.9.6 dated 2010-03-13

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

Package Rsolnp updated to version 1.0-2 with previous version 1.0 dated 2010-03-05

Title: General Non-linear Optimization
Description: General Non-linear Optimization Using Augmented Lagrange Multiplier Method
Author: Alexios Ghalanos and Stefan Theussl
Maintainer: Alexios Ghalanos

Diff between Rsolnp versions 1.0 dated 2010-03-05 and 1.0-2 dated 2010-03-13

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

Package Rcpp updated to version 0.7.9 with previous version 0.7.8 dated 2010-03-09

Title: Rcpp R/C++ interface package
Description: Seamless R and C++ integration The Rcpp package contains a C++ library that facilitates the integration of R and C++ in various ways. 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 underlying C++ library also offers the Rcpp::wrap function which is a templated function that transforms an arbitrary object into a SEXP. This makes it straightforward to implement C++ logic in terms of standard C++ types such as STL containers and then wrap them when they need to be returned to R. Internally, wrap uses advanced template meta programming techniques and currently supports : primitive types (bool, int, double, size_t, Rbyte, Rcomplex, std::string), STL containers (e.g std::vector) where T is wrappable, STL maps (e.g std::map) where T is wrappable, and arbitrary types that support implicit conversion to SEXP. The reverse conversion (from R to C++) is performed by the Rcpp::as function template offering a similar degree of flexibility. The package also contains a set of classes---which we call the `classic Rcpp API'---that were provided in an earlier API for R and C++ integration. Due to its continued use, the classic API is retained and will be supported for the foreseable future. The classic API includes support for R types real, integer, character, vector, matrix, Date, datetime (i.e. POSIXct) at microsecond resolution, data frame, and function. Transfer to and from simple or complex SEXP objects is made easy thanks to automatic conversion made possible by C++ template conversion. Calling R functions from C++ is also supported. C++ code can be 'inlined' by using the 'inline' package which will create a C++ function and compile, link and load it given the 'inlined' character argument which makes C++ integration very easy. Several examples are included, and over 150 unit tests provide addtional usage examples.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Simon Urbanek and David Reiss; based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel and Romain Francois

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

Package RcmdrPlugin.MAc updated to version 1.0.6 with previous version 1.0.5 dated 2010-03-01

Title: Meta-Analysis with Correlations (MAc) Rcmdr Plug-in
Description: This is an R-Commander plug-in for the MAc package (Meta-Analysis with Correlations). This package enables the user to conduct a meta-analysis in a menu-driven, graphical user interface environment (e.g., SPSS), while having the full statistical capabilities of R and the MAc package. The MAc package itself contains a variety of useful functions for conducting a research synthesis with correlational data. One of the unique features of the MAc package is in its integration of user-friendly functions to complete the majority of statistical steps involved in a meta-analysis with correlations. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re
Maintainer: AC Del Re

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More information about RcmdrPlugin.MAc at CRAN
Path: /cran/updated | permanent link

Package MplusAutomation updated to version 0.2-3 with previous version 0.2-2 dated 2010-03-11

Title: Automating Mplus Model Estimation and Interpretation
Description: The MplusAutomation package leverages the flexibility of the R language to automate latent variable model estimation and interpretation using Mplus, a powerful latent variable modeling program developed by Muthen and Muthen (www.statmodel.com). Specifically, MplusAutomation provides routines for creating related groups of models, running batches of models, and extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist
Maintainer: Michael Hallquist

Diff between MplusAutomation versions 0.2-2 dated 2010-03-11 and 0.2-3 dated 2010-03-13

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

Package MAd updated to version 0.2 with previous version 0.1 dated 2010-03-07

Title: Meta-Analysis with Mean Differences
Description: This is an integrated meta-analysis package for conducting a research synthesis with mean differences data. One of the unique features of this package is in its integration of user-friendly functions to complete most of the statistical steps involved in a meta-analysis with mean differences. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re & William T. Hoyt
Maintainer: AC Del Re

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

Package MAc updated to version 1.0.6 with previous version 1.0.5 dated 2010-03-01

Title: Meta-Analysis with Correlations
Description: This is an integrated meta-analysis package for conducting a research synthesis with correlational data. One of the unique features of this package is in its integration of user-friendly functions to complete the majority of statistical steps involved in a meta-analysis with correlations. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re & William T. Hoyt
Maintainer: AC Del Re

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Package AlgDesign updated to version 1.1-2 with previous version 1.1-1 dated 2010-01-25

Title: Algorithmic Experimental Design
Description: Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.
Author: Bob Wheeler
Maintainer: Bob Wheeler

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Path: /cran/updated | permanent link

Fri, 12 Mar 2010

Package betareg updated to version 2.2-0 with previous version 2.1-2 dated 2009-12-14

Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions.
Author: Achim Zeileis [aut, cre], Francisco Cribari-Neto [ctb], Alexandre B. Simas [ctb] (earlier version by), Andrea V. Rocha [ctb] (earlier version by)
Maintainer: Achim Zeileis

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Path: /cran/updated | permanent link

Package trio updated to version 1.0.15 with previous version 1.0.14 dated 2010-03-08

Title: Processing and Simulating Genotype Data for Trio Logic Regression
Description: Set up matched case-pseudo controls genotypes data for trios in order to run trio logic regreesion, to impute missing genotypes in trios, or to simulate case-parent trios with disease risk dependent on SNP-SNP interaction. This package furthermore contains functions for computing the values of pairwise LD measures and for identifying LD blocks.
Author: Qing Li, Holger Schwender
Maintainer: Qing Li

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Package TGUITeaching updated to version 0.9.5 with previous version 0.9.3 dated 2009-11-23

Title: Teaching GUI - prototype
Description: Trainings-GUI
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard Meindl
Maintainer: Bernhard Meindl

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Package R2HTML updated to version 2.0.0 with previous version 1.59-1 dated 2009-03-29

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).
Author: Eric Lecoutre
Maintainer: Eric Lecoutre

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Package GeoXp updated to version 1.4.3 with previous version 1.4.2 dated 2010-03-10

Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics, spatial econometrics, geography, ecology etc allowing to link dynamically statistical plots with elementary maps. This coupling consists in the fact that the selection of a zone on the map results in the automatic highlighting of the corresponding points on the statistical graph or reversely the selection of a portion of the graph results in the automatic highlighting of the corresponding points on the map. GeoXp includes tools from different areas of spatial statistics including geostatistics as well as spatial econometrics and point processes. Besides elementary plots like boxplots, histograms or simple scatterplos, GeoXp also couples with maps Moran scatterplots, variogram cloud, Lorentz Curves,...In order to make the most of the multidimensionality of the data, GeoXp includes some dimension reduction techniques such as PCA.
Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne Ruiz-Gazen, Christine Thomas-Agnan
Maintainer: Thibault Laurent

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Package Deducer updated to version 0.2-3 with previous version 0.2-2 dated 2009-12-23

Title: Deducer
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows
Maintainer: Ian Fellows

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Thu, 11 Mar 2010

Package oc updated to version 0.07 with previous version 0.04 dated 2008-09-03

Title: OC Roll Call Analysis Software.
Description: Estimates Optimal Classification scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
Author: Keith Poole , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: Jeffrey Lewis

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Package MplusAutomation updated to version 0.2-2 with previous version 0.2-1 dated 2010-03-10

Title: Automating Mplus Model Estimation and Interpretation
Description: The MplusAutomation package leverages the flexibility of the R language to automate latent variable model estimation and interpretation using Mplus, a powerful latent variable modeling program developed by Muthen and Muthen (www.statmodel.com). Specifically, MplusAutomation provides routines for creating related groups of models, running batches of models, and extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist
Maintainer: Michael Hallquist

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Package memisc updated to version 0.95-26 with previous version 0.95-23 dated 2009-11-12

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.
Author: Martin Elff
Maintainer: Martin Elff

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Package RFOC updated to version 1.0-9 with previous version 1.0-6 dated 2009-10-15

Title: Graphics for Spherical Distributions and Earthquake Focal Mechanisms
Description: Graphics for statistics on a sphere, as applied to geological fault data, crystalogaphy, earthquake focal mechanisms, radiation patterns, ternary plots and geographical/geological maps.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

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Package RFLPtools updated to version 1.1 with previous version 1.0 dated 2010-02-10

Title: Tools to analyse RFLP data
Description: RFLPtools provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
Author: Fabienne Flessa, Alexandra Kehl, Matthias Kohl
Maintainer: Matthias Kohl

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Package MKmisc updated to version 0.6.1 with previous version 0.5 dated 2010-02-10

Title: Miscellaneous Functions from M. Kohl
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl
Maintainer: Matthias Kohl

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Package sdef updated to version 1.5 with previous version 1.4 dated 2010-03-02

Title: Synthesizing List of Differentially Expressed Features
Description: The package performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments.
Author: Alberto Cassese, Marta Blangiardo
Maintainer: Alberto Cassese

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Package pyramid updated to version 1.2 with previous version 1.1 dated 2010-01-06

Title: Functions to draw population pyramid
Description: Drawing population pyramid using (1) data.frame or (2) vectors. The former is named as pyramid() and the latter pyramids(), as lapper function of pyramid().
Author: Minato Nakazawa
Maintainer: Minato Nakazawa

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Package interval updated to version 0.9-9.6 with previous version 0.9-9.5 dated 2010-02-03

Title: Weighted Logrank Tests and NPMLE for interval censored data
Description: Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay

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Package hergm updated to version 1.1 with previous version 1.0 dated 2010-02-21

Title: Hierarchical Exponential-Family Random Graph Models
Description: The R package 'hergm' implements Hierarchical Exponential-Family Random Graph Models (HERGMs), which can be used to model a wide range of relational data (networks). 'hergm' implements both simulation and Bayesian inference.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger

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Package TeachingSampling updated to version 1.4.9 with previous version 1.1.9 dated 2010-01-18

Title: Sampling designs and parameter estimation in finite population
Description: Foundations of inference in survey sampling
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas

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Wed, 10 Mar 2010

Package extremevalues updated to version 2.0 with previous version 1.0 dated 2009-12-03

Title: Univariate outlier detection
Description: Detect extreme values in onedimensional data
Author: Mark van der Loo
Maintainer: Mark van der Loo

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Path: /cran/updated | permanent link

Package RSQLite updated to version 0.8-4 with previous version 0.8-3 dated 2010-02-11

Title: SQLite interface for R
Description: Database Interface R driver for SQLite. This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.6.22) is included.
Author: David A. James
Maintainer: Seth Falcon

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

Package GeoXp updated to version 1.4.2 with previous version 1.4.1 dated 2010-03-10

Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics, spatial econometrics, geography, ecology etc allowing to link dynamically statistical plots with elementary maps. This coupling consists in the fact that the selection of a zone on the map results in the automatic highlighting of the corresponding points on the statistical graph or reversely the selection of a portion of the graph results in the automatic highlighting of the corresponding points on the map. GeoXp includes tools from different areas of spatial statistics including geostatistics as well as spatial econometrics and point processes. Besides elementary plots like boxplots, histograms or simple scatterplos, GeoXp also couples with maps Moran scatterplots, variogram cloud, Lorentz Curves,...In order to make the most of the multidimensionality of the data, GeoXp includes some dimension reduction techniques such as PCA.
Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne Ruiz-Gazen, Christine Thomas-Agnan
Maintainer: Thibault Laurent

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

Package topicmodels updated to version 0.0-4 with previous version 0.0-3 dated 2009-11-06

Title: Topic models
Description: Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan.
Author: Bettina Gruen and Kurt Hornik
Maintainer: Bettina Gruen

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

Package corpcor updated to version 1.5.6 with previous version 1.5.5 dated 2010-01-14

Title: Efficient Estimation of Covariance and (Partial) Correlation
Description: This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. The details of the method are explained in Sch\"afer and Strimmer (2005) and Opgen-Rhein and Strimmer (2007). The approach is both computationally as well as statistically very efficient, it is applicable to "small n, large p" data, and always returns a positive definite and well-conditioned covariance matrix. In addition to inferring the covariance matrix the package also provides shrinkage estimators for partial correlations, partial variances, and regression coefficients. The inverse of the covariance and correlation matrix can be efficiently computed, and as well as any arbitrary power of the shrinkage correlation matrix. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

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

Package survey updated to version 3.21 with previous version 3.20 dated 2010-02-09

Title: analysis of complex survey samples
Description: Summary statistics, generalised linear models, cumulative link 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 subsampling designs. Graphics. Predictive margins by direct standardization. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: Thomas Lumley

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

Package spatstat updated to version 1.18-0 with previous version 1.17-6 dated 2010-02-09

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. Also supports three-dimensional point patterns. 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, pixel images and tessellations. 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).
Author: Adrian Baddeley and Rolf Turner , with substantial contributions of code by Marie-Colette van Lieshout, Rasmus Waagepetersen, Kasper Klitgaard Berthelsen, Dominic Schuhmacher and Ege Rubak. Additional contributions by Ang Qi Wei, C. Beale, R. Bernhardt, B. Biggerstaff, R. Bivand, F. Bonneu, J. Burgos, S. Byers, J.B. Chen, Y.C. Chin, B. Christensen, M. de la Cruz, P. Dalgaard, 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, R. Mark, J. Mateu, P. McCullagh, S. Meyer, X.C. Mi, J. Moller, L.S. Nielsen, F. Nunes, E. Parilov, J. Picka, A. Raftery, 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, T. Verbeke, A. Villers, H. Wang, H. Wendrock and S. Wong.
Maintainer: Adrian Baddeley

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

Package simecol updated to version 0.6-10 with previous version 0.6-9 dated 2009-09-04

Title: Simulation of ecological (and other) dynamic systems
Description: simecol is an object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. The package helps to organize scenarios (avoids copy and paste) and improves readability and usability of code.
Author: Thomas Petzoldt
Maintainer: Thomas Petzoldt

Diff between simecol versions 0.6-9 dated 2009-09-04 and 0.6-10 dated 2010-03-10

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

Package mboost updated to version 2.0-3 with previous version 2.0-2 dated 2010-03-05

Title: Model-Based Boosting
Description: Functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn, Peter Buehlmann, Thomas Kneib, Matthias Schmid and Benjamin Hofner
Maintainer: Torsten Hothorn

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

Package ibr updated to version 1.2.1 with previous version 1.2 dated 2009-11-16

Title: Iterative Bias Reduction
Description: an R package for multivariate smoothing
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: Pierre-Andre Cornillon

Diff between ibr versions 1.2 dated 2009-11-16 and 1.2.1 dated 2010-03-10

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

Package GeoXp updated to version 1.4.1 with previous version 1.4 dated 2009-11-05

Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics, spatial econometrics, geography, ecology etc allowing to link dynamically statistical plots with elementary maps. This coupling consists in the fact that the selection of a zone on the map results in the automatic highlighting of the corresponding points on the statistical graph or reversely the selection of a portion of the graph results in the automatic highlighting of the corresponding points on the map. GeoXp includes tools from different areas of spatial statistics including geostatistics as well as spatial econometrics and point processes. Besides elementary plots like boxplots, histograms or simple scatterplos, GeoXp also couples with maps Moran scatterplots, variogram cloud, Lorentz Curves,...In order to make the most of the multidimensionality of the data, GeoXp includes some dimension reduction techniques such as PCA.
Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne Ruiz-Gazen, Christine Thomas-Agnan
Maintainer: Thibault Laurent

Diff between GeoXp versions 1.4 dated 2009-11-05 and 1.4.1 dated 2010-03-10

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

Tue, 09 Mar 2010

Package randomSurvivalForest updated to version 3.6.2 with previous version 3.6.1 dated 2010-01-27

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

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

Package pmg updated to version 0.9-42 with previous version 0.9-41 dated 2009-12-10

Title: Poor Man's GUI
Description: Simple GUI for R using gWidgets.
Author: John Verzani with contributions by Yvonnick Noel
Maintainer: John Verzani

Diff between pmg versions 0.9-41 dated 2009-12-10 and 0.9-42 dated 2010-03-09

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

Package ks updated to version 1.6.11 with previous version 1.6.10 dated 2010-02-24

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

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

Package gWidgetsRGtk2 updated to version 0.0-62 with previous version 0.0-61 dated 2010-03-07

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

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More information about gWidgetsRGtk2 at CRAN
Path: /cran/updated | permanent link

Package Rcpp updated to version 0.7.8 with previous version 0.7.7 dated 2010-02-14

Title: Rcpp R/C++ interface package
Description: Seamless R and C++ integration The Rcpp package contains a C++ library that facilitates the integration of R and C++ in various ways. 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 underlying C++ library also offers the Rcpp::wrap function which is a templated function that transforms an arbitrary object into a SEXP. This makes it straightforward to implement C++ logic in terms of standard C++ types such as STL containers and then wrap them when they need to be returned to R. Internally, wrap uses advanced template meta programming techniques and currently supports : primitive types (bool, int, double, size_t, Rbyte, Rcomplex, std::string), STL containers (e.g std::vector) where T is wrappable, STL maps (e.g std::map) where T is wrappable, and arbitrary types that support implicit conversion to SEXP. The reverse conversion (from R to C++) is performed by the Rcpp::as function template offering a similar degree of flexibility. The package also contains a set of classes---which we call the `classic Rcpp API'---that were provided in an earlier API for R and C++ integration. Due to its continued use, the classic API is retained and will be supported for the foreseable future. The classic API includes support for R types real, integer, character, vector, matrix, Date, datetime (i.e. POSIXct) at microsecond resolution, data frame, and function. Transfer to and from simple or complex SEXP objects is made easy thanks to automatic conversion made possible by C++ template conversion. Calling R functions from C++ is also supported. C++ code can be 'inlined' by using the 'inline' package which will create a C++ function and compile, link and load it given the 'inlined' character argument which makes C++ integration very easy. Several examples are included, and over 150 unit tests provide addtional usage examples.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Simon Urbanek and David Reiss; based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel and Romain Francois

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

Package DiagnosisMed updated to version 0.2.3 with previous version 0.2.2.2 dated 2009-08-25

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 able to estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different categorical tests, and estimate reasonble cut-offs of tests and display it in a way commonly used by health professionals. No graphical interface is avalible yet. Partners are most welcome.
Author: Pedro Brasil
Maintainer: Pedro Brasil

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

Package pcaPP updated to version 1.8 with previous version 1.7 dated 2009-07-18

Title: Robust PCA by Projection Pursuit
Description: Robust PCA by Projection Pursuit
Author: Peter Filzmoser Heinrich Fritz Klaudius Kalcher
Maintainer: Peter Filzmoser

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

Package monomvn updated to version 1.8-1 with previous version 1.8 dated 2010-01-14

Title: Estimation for multivariate normal and Student-t data with monotone missingness
Description: Estimation of multivariate normal and student-t data of arbitrary dimension where the pattern of missing data is monotone. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle a nearly arbitrary amount of missing data. The current version supports maximum likelihood inference and a full Bayesian approach employing scale-mixtures for the lasso (double-exponential) and Normal-Gamma priors, and Student-t errors. Monotone data augmentation extends this Bayesian approach to arbitrary missingness patterns. A fully functional standalone interface to the Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown), and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy

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

Package chemometrics updated to version 0.8 with previous version 0.7 dated 2010-03-04

Title: Multivariate Statistical Analysis in Chemometrics
Description: This package is the R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)
Author: P. Filzmoser and K. Varmuza
Maintainer: P. Filzmoser

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

Package BradleyTerry updated to version 0.8-8 with previous version 0.8-7 dated 2008-07-11

Title: Bradley-Terry Models -- this package is now deprecated in favour of 'BradleyTerry2'
Description: Specify and fit the Bradley-Terry model and structured versions
Author: David Firth
Maintainer: David Firth

Diff between BradleyTerry versions 0.8-7 dated 2008-07-11 and 0.8-8 dated 2010-03-09

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

Package spBayes updated to version 0.1-6 with previous version 0.1-5 dated 2010-01-08

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

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Package sp updated to version 0.9-61 with previous version 0.9-60 dated 2010-02-15

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

Diff between sp versions 0.9-60 dated 2010-02-15 and 0.9-61 dated 2010-03-09

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Package rsprng updated to version 1.0 with previous version 0.4 dated 2008-06-08

Title: R interface to SPRNG (Scalable Parallel Random Number Generators)
Description: Provides interface to SPRNG 2.0 APIs, and examples and documentation for its use.
Author: Na (Michael) Li
Maintainer: Na (Michael) Li

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Package sbgcop updated to version 0.975 with previous version 0.95 dated 2007-03-09

Title: Semiparametric Bayesian Gaussian copula estimation and imputation
Description: This package estimates parameters of a Gaussian copula, treating the univariate marginal distributions as nuisance parameters as described in Hoff(2007). It also provides a semiparametric imputation procedure for missing multivariate data.
Author: Peter Hoff
Maintainer: Peter Hoff

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Package mc2d updated to version 0.1-7 with previous version 0.1-6 dated 2009-09-12

Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: Various distributions and utilities to ease the use of R to build and study Two-Dimensional Monte-Carlo simulations
Author: Regis Pouillot , Marie Laure Delignette-Muller and Jean-Baptiste Denis
Maintainer: Regis Pouillot

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Package far updated to version 0.6-3 with previous version 0.6-2 dated 2007-10-02

Title: Modelization for Functional AutoRegressive processes
Description: Modelizations and previsions functions for Functional AutoRegressive processes using nonparametric methods: functional kernel, estimation of the covariance operator in a subspace, ...
Author: Damon Julien Guillas Serge
Maintainer: Damon Julien

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Package FD updated to version 1.0-7 with previous version 1.0-5 dated 2009-11-30

Title: Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology
Description: FD is a package to compute different multidimensional FD indices. It implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. It also contains other useful tools for functional ecology.
Author: Etienne Laliberté, Bill Shipley
Maintainer: Etienne Laliberté

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Package CADStat updated to version 2.2-2 with previous version 2.1-21 dated 2009-06-29

Title: Provides a GUI to several statistical methods useful for causal assessment.
Description: Using JGR, provides a GUI to several statistical methods - scatterplot, boxplot, linear regression, generalized linear regression, quantile, regression, conditional probability calculations, and regression trees.
Author: Lester Yuan, Tom Stockton, Doug Bronson, Pasha Minallah, and Mark Fitzgerald
Maintainer: Lester Yuan

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Mon, 08 Mar 2010

Package vegan updated to version 1.17-2 with previous version 1.17-1 dated 2010-02-18

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen

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Package trio updated to version 1.0.14 with previous version 1.0.13 dated 2010-03-04

Title: Processing and Simulating Genotype Data for Trio Logic Regression
Description: Set up matched case-pseudo controls genotypes data for trios in order to run trio logic regreesion, to impute missing genotypes in trios, or to simulate case-parent trios with disease risk dependent on SNP-SNP interaction. This package furthermore contains functions for computing the values of pairwise LD measures and for identifying LD blocks.
Author: Qing Li, Holger Schwender
Maintainer: Qing Li

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Package ipw updated to version 1.0-4 with previous version 1.0-3 dated 2010-03-05

Title: Estimate inverse probability weights.
Description: Estimate inverse probability weights. These are typically used to perform inverse probability weighting (IPW) to fit a marginal structural model (MSM), to estimate causal effects from observational data. Both data from point treatment situations and longitudinal studies can be used.
Author: Willem M. van der Wal
Maintainer: Willem M. van der Wal

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Package dynGraph updated to version 0.99100403 with previous version 0.99070509 dated 2009-05-17

Title: Interactive visualization of dataframes and factorial planes
Description: Interactive visualization of dataframes and factorial planes
Author: Sebastien Le, Julien Durand
Maintainer: Sebastien Le

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Package bio.infer updated to version 1.2-8 with previous version 1.2-7 dated 2010-02-28

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

Diff between bio.infer versions 1.2-7 dated 2010-02-28 and 1.2-8 dated 2010-03-08

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Path: /cran/updated | permanent link

Package relations updated to version 0.5-7 with previous version 0.5-6 dated 2010-02-10

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: Kurt Hornik and David Meyer
Maintainer: Kurt Hornik

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Package lda updated to version 1.2 with previous version 1.1 dated 2009-09-29

Title: Collapsed Gibbs sampling methods for topic models.
Description: This package implements latent Dirichlet allocation (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler writtten in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.
Author: Jonathan Chang
Maintainer: Jonathan Chang

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Package animation updated to version 1.1-0 with previous version 1.0-10 dated 2009-12-02

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.
Author: Yihui Xie
Maintainer: Yihui Xie

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Sun, 07 Mar 2010

Package arulesSequences updated to version 0.1-9 with previous version 0.1-8 dated 2009-06-15

Title: Mining frequent sequences
Description: Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta

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 7 files changed, 16 insertions(+), 12 deletions(-)

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

Package REQS updated to version 0.8-6 with previous version 0.8-5 dated 2009-11-19

Title: R/EQS Interface
Description: This package contains the function run.eqs() which calls an EQS script file, executes the EQS estimation, and, finally, imports the results as R objects. These two steps can be performed separately: call.eqs() calls and executes EQS, whereas read.eqs() imports existing EQS outputs as objects into R.
Author: Patrick Mair, Eric Wu
Maintainer: Eric Wu

Diff between REQS versions 0.8-5 dated 2009-11-19 and 0.8-6 dated 2010-03-07

 DESCRIPTION  |    8 ++++----
 R/read.eqs.R |   39 +++++++++++++++++++++++++++------------
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More information about REQS at CRAN
Path: /cran/updated | permanent link

Package vcdExtra updated to version 0.4-1 with previous version 0.4-0 dated 2010-02-28

Title: vcd additions
Description: Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data.
Author: Michael Friendly with Heather Turner, David Firth and Achim Zeileis
Maintainer: Michael Friendly

Diff between vcdExtra versions 0.4-0 dated 2010-02-28 and 0.4-1 dated 2010-03-07

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 NAMESPACE                              |   12 +++--
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More information about vcdExtra at CRAN
Path: /cran/updated | permanent link

Package rbenchmark updated to version 0.3 with previous version 0.2 dated 2009-03-27

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.
Author: Wacek Kusnierczyk
Maintainer: Wacek Kusnierczyk

Diff between rbenchmark versions 0.2 dated 2009-03-27 and 0.3 dated 2010-03-07

 DESCRIPTION              |    8 ++++----
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 4 files changed, 23 insertions(+), 15 deletions(-)

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

Package rattle updated to version 2.5.24 with previous version 2.5.23 dated 2010-03-04

Title: A graphical user interface for data mining in R using Gnome
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.
Author: Graham Williams
Maintainer: Graham Williams

Diff between rattle versions 2.5.23 dated 2010-03-04 and 2.5.24 dated 2010-03-07

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

Package pgirmess updated to version 1.4.4 with previous version 1.4.3 dated 2009-12-11

Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of ecological and spatial data
Author: Patrick Giraudoux
Maintainer: Patrick Giraudoux

Diff between pgirmess versions 1.4.3 dated 2009-12-11 and 1.4.4 dated 2010-03-07

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

Package isopam updated to version 0.9-6 with previous version 0.9-5 dated 2010-02-18

Title: Isopam (Hierarchical Clustering)
Description: Isopam clustering algorithm and utilities. Isopam optimizes clusters and optionally cluster numbers in a brute force style and aims at an optimum separation by a limited number of indicative descriptors (typically species).
Author: Sebastian Schmidtlein with contributions from Jason Collison
Maintainer: Sebastian Schmidtlein

Diff between isopam versions 0.9-5 dated 2010-02-18 and 0.9-6 dated 2010-03-07

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

Package gWidgetsRGtk2 updated to version 0.0-61 with previous version 0.0-59 dated 2010-02-13

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 0.0-59 dated 2010-02-13 and 0.0-61 dated 2010-03-07

 ChangeLog                    |   11 +++++++++++
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More information about gWidgetsRGtk2 at CRAN
Path: /cran/updated | permanent link

Package diffractometry updated to version 0.1-02 with previous version 0.1-00 dated 2008-06-13

Title: Baseline identification and peak decomposition for x-ray diffractograms
Description: Residual-based baseline identification and peak decomposition for x-ray diffractograms as introduced in Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger. Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger

Diff between diffractometry versions 0.1-00 dated 2008-06-13 and 0.1-02 dated 2010-03-07

 DESCRIPTION                   |   26 ++++++++------
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More information about diffractometry at CRAN
Path: /cran/updated | permanent link

Fri, 05 Mar 2010

Package caGUI updated to version 0.1-4 with previous version 0.1-3 dated 2010-03-01

Title: A Tcl/Tk GUI for the functions in the ca package
Description: A Graphical User Interface (GUI) for computation and visualization of simple, multiple and joint correspondence analysis with the ca package.
Author: Angelos Markos
Maintainer: Angelos Markos

Diff between caGUI versions 0.1-3 dated 2010-03-01 and 0.1-4 dated 2010-03-05

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

Package tmvtnorm updated to version 1.0-2 with previous version 1.0-1 dated 2010-03-04

Title: Truncated Multivariate Normal and Student t Distribution
Description: Random number generation for the truncated multivariate normal and Student t distribution. Computes probabilities, quantiles and densities, including one-dimensional and bivariate marginal densities. Computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.
Author: Stefan Wilhelm with contributions from Manjunath B G
Maintainer: Stefan Wilhelm

Diff between tmvtnorm versions 1.0-1 dated 2010-03-04 and 1.0-2 dated 2010-03-05

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

Package integrativeME updated to version 1.2 with previous version 1.1 dated 2009-10-14

Title: integrative mixture of experts
Description: Mixture of experts models (Jacobs et al., 1991) were introduced to account for nonlinearities and other complexities in the data. It is based on a divide-and-conquer strategy. Mixture of experts are of interest due to their wide applicability and the advantages of fast learning via the expectation-maximization (EM) algorithm. We have extended and implemented mixture of experts to combine categorical clinical factors and continuous microarray data in a binary classification framework to analyze cancer studies. To provide a hybrid signature of clinical factors and gene markers, we propose to apply different gene selection procedures as a first step.
Author: Kim-Anh Le Cao
Maintainer: Kim-Anh Le Cao

Diff between integrativeME versions 1.1 dated 2009-10-14 and 1.2 dated 2010-03-05

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

Package gRapHD updated to version 0.1.6 with previous version 0.1.5 dated 2010-01-20

Title: Efficient selection of undirected graphical models for high-dimensional datasets
Description: gRapHD is designed for efficient selection of high-dimensional undirected graphical models. The package provides tools for selecting trees, forests and decomposable models minimizing information criteria such as AIC or BIC, and for displaying the independence graphs of the models. It has also some useful tools for analysing graphical structures. It supports the use of discrete, continuous, or both types of variables.
Author: Gabriel Coelho Goncalves de Abreu , Rodrigo Labouriau , David Edwards .
Maintainer: Gabriel Coelho Goncalves de Abreu

Diff between gRapHD versions 0.1.5 dated 2010-01-20 and 0.1.6 dated 2010-03-05

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

Package dplR updated to version 1.2.9 with previous version 1.2.8 dated 2010-02-28

Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some standard tree-ring analyses.
Author: Andy Bunn with contributions from Mikko Korpela, Franco Biondi, and Christain Zang
Maintainer: Andy Bunn

Diff between dplR versions 1.2.8 dated 2010-02-28 and 1.2.9 dated 2010-03-05

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

Package DEoptim updated to version 2.0-4 with previous version 2.0-3 dated 2009-11-29

Title: Global optimization by differential evolution
Description: This package provides the DEoptim function which performs global optimization by differential evolution.
Author: David Ardia and Katharine Mullen
Maintainer: Katharine Mullen

Diff between DEoptim versions 2.0-3 dated 2009-11-29 and 2.0-4 dated 2010-03-05

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

Package seacarb updated to version 2.3.2 with previous version 2.3.1 dated 2010-01-26

Title: Calculates parameters of the seawater carbonate system
Description: Calculates parameters of the seawater carbonate system
Author: Heloise Lavigne and Jean-Pierre Gattuso. Portions of code and/or corrections were contributed by Jean-Marie Epitalon, Bernard Gentili, Andreas Hofmann, Jim Orr, Aurelien Proye, and Karline Soetaert
Maintainer: Jean-Pierre Gattuso

Diff between seacarb versions 2.3.1 dated 2010-01-26 and 2.3.2 dated 2010-03-05

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

Package party updated to version 0.9-9993 with previous version 0.9-9992 dated 2010-02-26

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

Diff between party versions 0.9-9992 dated 2010-02-26 and 0.9-9993 dated 2010-03-05

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 src/RandomForest.c                                                                   |    2 
 src/Utils.c                                                                          |   16 +-
 src/Utils.h                                                                          |    2 
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More information about party at CRAN
Path: /cran/updated | permanent link

Package mboost updated to version 2.0-2 with previous version 2.0-1 dated 2010-03-01

Title: Model-Based Boosting
Description: Functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn, Peter Buehlmann, Thomas Kneib, Matthias Schmid and Benjamin Hofner
Maintainer: Torsten Hothorn

Diff between mboost versions 2.0-1 dated 2010-03-01 and 2.0-2 dated 2010-03-05

 DESCRIPTION                       |   10 +++++-----
 NEWS                              |   21 +++++++++++++++------
 R/btree.R                         |    2 +-
 R/helpers.R                       |    6 +-----
 inst/CHANGES                      |   21 +++++++++++++++------
 inst/doc/SurvivalEnsembles.pdf    |binary
 inst/doc/mboost_illustrations.pdf |binary
 man/mboost_package.Rd             |    4 ++--
 tests/bugfixes.R                  |   22 ++++++++++++++++++++++
 tests/bugfixes.Rout.save          |   22 ++++++++++++++++++++++
 10 files changed, 83 insertions(+), 25 deletions(-)

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

Package ipw updated to version 1.0-3 with previous version 1.0-2 dated 2010-02-14

Title: Estimate inverse probability weights.
Description: Estimate inverse probability weights. These are typically used to perform inverse probability weighting (IPW) to fit a marginal structural model (MSM), to estimate causal effects from observational data. Both data from point treatment situations and longitudinal studies can be used.
Author: Willem M. van der Wal
Maintainer: Willem M. van der Wal

Diff between ipw versions 1.0-2 dated 2010-02-14 and 1.0-3 dated 2010-03-05

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 ipw-1.0-3/ipw/man/ipwtm.Rd       |   58 ++++-------------------------------
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 ipw-1.0-3/ipw/man/tstartfun.Rd   |    4 +-
 10 files changed, 51 insertions(+), 96 deletions(-)

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

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