Fri, 26 Nov 2010

Package selectMeta updated to version 1.0.1 with previous version 1.0.0 dated 2010-11-15

Title: Estimation weight functions in meta analysis
Description: Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. In this package we provide implementations of several parametric and nonparametric weight functions. The novelty in Rufibach (2010) is the proposal of a non-increasing variant of the nonparametric weight function of Dear & Begg (1992). The new approach potentially offers more insight in the selection process than other methods, but is more flexible than parametric approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992) under a monotonicity constraint we use a differential evolution algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al (2009).
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach

Diff between selectMeta versions 1.0.0 dated 2010-11-15 and 1.0.1 dated 2010-11-26

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 12 files changed, 26 insertions(+), 14 deletions(-)

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Package gee updated to version 4.13-16 with previous version 4.13-15 dated 2010-07-27

Title: Generalized Estimation Equation solver
Description: Generalized Estimation Equation solver
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and 4.4) and Brian Ripley (version 4.13).
Maintainer: Brian Ripley

Diff between gee versions 4.13-15 dated 2010-07-27 and 4.13-16 dated 2010-11-26

 ChangeLog   |    4 ++++
 DESCRIPTION |    9 +++++----
 R/ugee.R    |    3 ++-
 3 files changed, 11 insertions(+), 5 deletions(-)

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New package directlabels with initial version 1.1
Package: directlabels
Maintainer: Toby Dylan Hocking
Author: Toby Dylan Hocking
Version: 1.1
License: GPL-3
Title: Direct labels for plots
Description: Direct labeling functions meant to be used with several plotting packages, including lattice and ggplot2.
URL: http://directlabels.r-forge.r-project.org/
LazyLoad: false
LazyData: true
Depends: proto
Suggests: ks, MASS, inlinedocs, quadprog, ggplot2, lattice, alphahull, ElemStatLearn
Imports: ggplot2
Collate: utility.function.R compare.R dotplot.R lineplot.R densityplot.R ggplot2.R positioning.functions.R doc.R lattice.R scatterplot.R contourplot.R
Packaged: 2010-11-26 15:31:32 UTC; hocking
Repository: CRAN
Date/Publication: 2010-11-26 16:37:05

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Package SSSR updated to version 1.0.3 with previous version 1.0.2 dated 2010-11-23

Title: Server Side Scripting with R
Description: This package is for using R as a server side scripting language with session, application and cookie support
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman

Diff between SSSR versions 1.0.2 dated 2010-11-23 and 1.0.3 dated 2010-11-26

 DESCRIPTION |    7 ++++---
 R/SSSR.r    |    2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

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Package RHmm updated to version 1.4.2 with previous version 1.3.4 dated 2010-11-15

Title: Hidden Markov Models simulations and estimations
Description: Discrete, univariate or multivariate gaussian, mixture of univariate or multivariate gaussian HMM functions for simulation and estimation.
Author: Ollivier TARAMASCO, Sebastian Bauer
Maintainer: Ollivier TARAMASCO , Sebastian Bauer

Diff between RHmm versions 1.3.4 dated 2010-11-15 and 1.4.2 dated 2010-11-26

 DESCRIPTION                     |   13 
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 README                          |    9 
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 60 files changed, 3961 insertions(+), 3793 deletions(-)

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New package DMwR with initial version 0.1.0
Package: DMwR
Type: Package
Title: Functions and data for "Data Mining with R"
Version: 0.1.0
Depends: R(>= 2.5), methods, graphics, xts (>= 0.6-7), quantmod (>= 0.3-8), ROCR (>= 1.0-2), class (>= 7.3-1), rpart (>= 3.1-46), abind (>= 1.1-0), cluster (>= 1.12.1), lattice (>= 0.18-3), grid (>= 2.10.1), zoo (>= 1.6-4)
Date: 2010-11-20
Author: Luis Torgo
Maintainer: Luis Torgo
Description: This package includes functions and data accompanying the book "Data Mining with R, learning with case studies" by Luis Torgo, CRC Press 2010.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2010-11-26 15:13:46 UTC; ltorgo
Repository: CRAN
Date/Publication: 2010-11-26 16:36:47

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Package hwriter updated to version 1.3 with previous version 1.2 dated 2010-03-17

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

Diff between hwriter versions 1.2 dated 2010-03-17 and 1.3 dated 2010-11-26

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New package mem with initial version 1.0
Package: mem
Type: Package
Title: Moving Epidemics Method R Package.
Version: 1.0
Date: 2010-11-26
Author: Jose E. Lozano Alonso
Maintainer: Jose E. Lozano Alonso
Depends: R (>= 2.12.0), sm, boot
Description: Modelization of influenza epidemics in order to monitor future activity.
License: GPL (>= 2)
Packaged: 2010-11-26 10:29:45 UTC; lozalojo
Repository: CRAN
Date/Publication: 2010-11-26 12:50:08

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Package SGP updated to version 0.0-6.5 with previous version 0.0-6.4 dated 2010-10-21

Title: Student Growth Percentile and Percentile Growth Projection/Trajectory Functions
Description: Functions to calculate student growth percentiles and percentile growth projections/trajectories for students using large scale, longitudinal assessment data. Functions use quantile regression to estimate the conditional density associated with each student's achievement history. Percentile growth projections/trajectories are calculated using the coefficient matrices derived from the quantile regression analyses and specify what percentile growth is required for students to reach future achievement targets.
Author: Damian W. Betebenner , with contributions from Adam Van Iwaarden, Jonathan Weeks, Jinnie Choi, Marie Huchton, Xin Wei, and Hi Shin Shim
Maintainer: Damian W. Betebenner

Diff between SGP versions 0.0-6.4 dated 2010-10-21 and 0.0-6.5 dated 2010-11-26

 DESCRIPTION                     |   12 ++--
 R/studentGrowthPercentiles.R    |   65 +++++++++++++++-----------
 R/studentGrowthProjections.R    |   41 ++++++++++------
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 man/studentGrowthProjections.Rd |    3 -
 10 files changed, 173 insertions(+), 73 deletions(-)

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New package DiceView with initial version 1.0-0
Package: DiceView
Title: Plot methods for computer experiments design and models.
Version: 1.0-0
Date: 2010-11-15
Author: Yann Richet, Yves Deville, Clement Chevalier
Maintainer: Yann Richet
Description: View 2D/3D sections of computer experiments designs and kriging models.
Depends: methods, DiceKriging, DiceEval, rgl
License: GPL-3
URL: http://www.dice-consortium.fr/
Repository: CRAN
Date/Publication: 2010-11-26 12:49:57
Packaged: 2010-11-26 10:40:19 UTC; yves

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Package pegas updated to version 0.3-3 with previous version 0.3-2 dated 2010-06-10

Title: Population and Evolutionary Genetics Analysis System
Description: pegas provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences including coalescence analyses.
Author: Emmanuel Paradis
Maintainer: Emmanuel Paradis

Diff between pegas versions 0.3-2 dated 2010-06-10 and 0.3-3 dated 2010-11-26

 ChangeLog                 |   17 +++++++++++++++++
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 12 files changed, 116 insertions(+), 53 deletions(-)

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Package mefa updated to version 3.1-6 with previous version 3.1-4 dated 2009-11-15

Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos

Diff between mefa versions 3.1-4 dated 2009-11-15 and 3.1-6 dated 2010-11-26

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Package doBy updated to version 4.1.2 with previous version 4.1.1 dated 2010-11-12

Title: Groupwise summary statistics, general linear contrasts, LSMEANS (least-squares-means), and other utilities
Description: Facilities for groupwise computations of summary statistics and other facilities for working with grouped data.
Author: Søren Højsgaard with contributions from Ulrich Halekoh, Jim Robison-Cox, Kevin Wright and Alessandro A. Leidi.
Maintainer: Søren Højsgaard

Diff between doBy versions 4.1.1 dated 2010-11-12 and 4.1.2 dated 2010-11-26

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Package RcppArmadillo updated to version 0.2.10 with previous version 0.2.9 dated 2010-11-12

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 1.0.0). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain, Dirk and Doug

Diff between RcppArmadillo versions 0.2.9 dated 2010-11-12 and 0.2.10 dated 2010-11-26

 ChangeLog                                               |   17 ++++++++
 DESCRIPTION                                             |   25 +++++------
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Package Boruta updated to version 1.4 with previous version 1.3 dated 2010-09-02

Title: Boruta -- a tool for finding significant attributes in information systems
Description: Boruta is a feature selection algorithm based on a randomForest predictor. It selects the full set of all important attributes by comparing original attributes importance with datum importance of their randomised copies.
Author: Algorithm by Witold R. Rudnicki , R implementation by Miron B. Kursa .
Maintainer: Miron B. Kursa

Diff between Boruta versions 1.3 dated 2010-09-02 and 1.4 dated 2010-11-26

 DESCRIPTION           |    8 ++++----
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 5 files changed, 36 insertions(+), 29 deletions(-)

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Package openair updated to version 0.3-25 with previous version 0.3-15 dated 2010-10-14

Title: Tools for the analysis of air pollution data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw and Karl Ropkins
Maintainer: David Carslaw

Diff between openair versions 0.3-15 dated 2010-10-14 and 0.3-25 dated 2010-11-26

 DESCRIPTION           |    8 -
 NAMESPACE             |    8 +
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 R/calcFno2.R          |   24 +++
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Package mnormt updated to version 1.3-4 with previous version 1.3-3 dated 2009-03-21

Title: The multivariate normal and t distributions
Description: This package provides functions for computing the density and the distribution function of multivariate normal and multivariate "t" distributions, and for generating random vectors sampled from these distributions. Probabilities are computed via a non-Monte Carlo method; different routines are used for the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between mnormt versions 1.3-3 dated 2009-03-21 and 1.3-4 dated 2010-11-26

 DESCRIPTION |   22 +++++++++++-----------
 R/mnormt.R  |    3 +--
 history.txt |    1 +
 3 files changed, 13 insertions(+), 13 deletions(-)

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Package gMCP updated to version 0.3-4 with previous version 0.3-3 dated 2010-11-15

Title: A graphical approach to sequentially rejective multiple test procedures
Description: This package provides functions and a graphical user interface for graphical described sequentially rejective multiple test procedures.
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer

Diff between gMCP versions 0.3-3 dated 2010-11-15 and 0.3-4 dated 2010-11-26

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 gMCP-0.3-4/gMCP/NEWS                                                                 |    7 +
 gMCP-0.3-4/gMCP/R/exampleGraphs.R                                                    |    2 
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 gMCP-0.3-4/gMCP/TODO                                                                 |    7 +
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 gMCP-0.3-4/gMCP/inst/doc/gMCP.pdf                                                    |binary
 gMCP-0.3-4/gMCP/inst/doc/pictures/FullFeaturedGUI.png                                |binary
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/CreateGraphGUI.java                     |   17 ++++
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/MenuBarMGraph.java                      |    4 -
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/CellEditorE.java              |    9 --
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/CellEditorEps.java            |    7 -
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/CellValue.java                |   12 ---
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/DataFramePanel.java           |   20 +----
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/DataTable.java                |   37 ----------
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/DataTableModel.java           |   15 ----
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/EpsilonTableCellRenderer.java |    1 
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/datatable/RDataFrameRef.java            |   10 --
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/ControlMGraph.java                |   22 +++++
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/DialogConfIntEstVar.java          |   16 +++-
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/Edge.java                         |    9 +-
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/GraphView.java                    |    2 
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/NetzListe.java                    |   15 +++-
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/PView.java                        |    2 
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/graph/UpdateEdge.java                   |   10 +-
 gMCP-0.3-4/gMCP/inst/java-src/org/mutoss/gui/options/GeneralPanel.java               |    1 
 gMCP-0.3-4/gMCP/inst/java/gsrmtp.jar                                                 |binary
 gMCP-0.3-4/gMCP/inst/unitTests/runit.graphGMCP.R                                     |only
 gMCP-0.3-4/gMCP/man/matrix2graph.Rd                                                  |only
 38 files changed, 152 insertions(+), 134 deletions(-)

More information about gMCP at CRAN
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Package depmixS4 updated to version 1.0-1 with previous version 1.0-0 dated 2010-08-05

Title: Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries) data, otherwise known as dependent mixture models
Author: Ingmar Visser , Maarten Speekenbrink
Maintainer: Ingmar Visser

Diff between depmixS4 versions 1.0-0 dated 2010-08-05 and 1.0-1 dated 2010-11-26

 DESCRIPTION             |   10 +++---
 NAMESPACE               |    3 +
 NEWS                    |   44 ++++++++++++++++++++++------
 R/EM.R                  |   59 ++++++++++++++++++++++++--------------
 R/depmixfit.R           |   18 +++++------
 R/em.control.R          |only
 R/makePriorModel.R      |    2 -
 R/makeTransModels.R     |    7 +---
 R/responseGLM.R         |    2 -
 R/responseGLMMULTINOM.R |    2 -
 inst/doc/depmixS4.Rnw   |   22 ++++++++------
 inst/doc/depmixS4.pdf   |binary
 man/GLMresponse.Rd      |   10 +++---
 man/depmix.fit.Rd       |   74 +++++++++---------------------------------------
 man/em.control.Rd       |only
 man/makeDepmix.Rd       |   35 ++++++++++++----------
 man/responses.Rd        |   38 ++++++++++++------------
 man/simulate.Rd         |    2 -
 man/transInit.Rd        |    2 -
 tests/test3responses.R  |    5 +--
 20 files changed, 168 insertions(+), 167 deletions(-)

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Package PowerTOST updated to version 0.8-1 with previous version 0.7-3 dated 2010-11-08

Title: Power and Sample size based on two one-sided t-tests (TOST) for bioequivalence studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval).
Author: Detlew Labes
Maintainer: D. Labes

Diff between PowerTOST versions 0.7-3 dated 2010-11-08 and 0.8-1 dated 2010-11-26

 DESCRIPTION              |    8 ++++----
 NEWS                     |    5 +++++
 R/CVfromCI.R             |only
 R/DesignHelpers.R        |   22 +++++++++++-----------
 R/SampleSize.R           |    2 +-
 R/expSampleSize.R        |    4 ++--
 R/exppower.R             |    4 ++--
 man/CVfromCI.Rd          |only
 man/PowerTOST-package.Rd |   12 ++++++------
 man/exppower.TOST.Rd     |    8 ++++----
 man/expsampleN.TOST.Rd   |    8 ++++----
 11 files changed, 39 insertions(+), 34 deletions(-)

More information about PowerTOST at CRAN
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