Mon, 03 Sep 2012

Package LaplacesDemon updated to version 12.09.03 with previous version 12.08.06 dated 2012-08-06

Title: Complete Environment for Bayesian Inference
Description: Laplace's Demon is a complete environment for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall

Diff between LaplacesDemon versions 12.08.06 dated 2012-08-06 and 12.09.03 dated 2012-09-03

 CHANGELOG                                 |    7 
 DESCRIPTION                               |    8 
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 NAMESPACE                                 |    6 
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Package PIPS updated to version 1.0.1 with previous version 1.0 dated 2012-02-12

Title: Predicted Interval Plots
Description: Generate Predicted Interval Plots. Simulate and plot confidence intervals of an effect estimate given observed data and a hypothesis about the distribution of future data.
Author: Daniel G. Muenz, Ray Griner , Huichao Chen, Lijuan Deng, Sachiko Miyahara, and Scott R. Evans , with contributions from Lingling Li, Hajime Uno, and Laura M. Smeaton.
Maintainer: Ray Griner

Diff between PIPS versions 1.0 dated 2012-02-12 and 1.0.1 dated 2012-09-03

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 12 files changed, 129 insertions(+), 67 deletions(-)

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Package TTAinterfaceTrendAnalysis updated to version 1.02 with previous version 1.01 dated 2012-03-22

Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure of temporal trend analysis in the framework of the OSPAR convention. It is based on 5 successive steps : simply manipulate your database, select the parameters you want to analyse, build your regulated time series, perform analysis and read the results all in one easy to use interface. Statistical analysis call other package function such as Kendall tests (wq package) or cusum function (Pastec package).
Author: David Devreker [aut], Alain Lefebvre [aut, cre]
Maintainer: Alain Lefebvre

Diff between TTAinterfaceTrendAnalysis versions 1.01 dated 2012-03-22 and 1.02 dated 2012-09-03

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Package StatDataML updated to version 1.0-22 with previous version 1.0-21 dated 2011-11-01

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

Diff between StatDataML versions 1.0-21 dated 2011-11-01 and 1.0-22 dated 2012-09-03

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Package SNPassoc updated to version 1.8-4 with previous version 1.8-1 dated 2011-11-22

Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno
Maintainer: Juan R González

Diff between SNPassoc versions 1.8-1 dated 2011-11-22 and 1.8-4 dated 2012-09-03

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Package pheatmap updated to version 0.7.2 with previous version 0.7.1 dated 2012-08-29

Title: Pretty Heatmaps
Description: A package for drawing pretty heatmaps in R. The ordinary heatmap function in R has several drawbacks when it comes to producing publication quality heatmaps. It is hard to produce pictures with consistent text, cell and overall sizes and shapes. The function pheatmap tries to alleviate the problems by offering more fine grained control over heatmap dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde

Diff between pheatmap versions 0.7.1 dated 2012-08-29 and 0.7.2 dated 2012-09-03

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Package mhsmm updated to version 0.4.6 with previous version 0.4.4 dated 2011-06-17

Title: Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences.
Description: Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data.
Author: Jared O'Connell , Søren Højsgaard
Maintainer: Jared O'Connell

Diff between mhsmm versions 0.4.4 dated 2011-06-17 and 0.4.6 dated 2012-09-03

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Package fingerprint updated to version 3.4.8.1 with previous version 3.4.7 dated 2012-02-27

Title: Functions to operate on binary fingerprint data
Description: This package contains functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint' which is internally represented a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.
Author: Rajarshi Guha
Maintainer: Rajarshi Guha

Diff between fingerprint versions 3.4.7 dated 2012-02-27 and 3.4.8.1 dated 2012-09-03

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Package normalp updated to version 0.6.9 with previous version 0.6.8 dated 2009-01-27

Title: Package for exponential power distributions (EPD)
Description: A collection of utilities referred to exponential power distributions, also known as General Error Distribution
Author: Angelo M. Mineo
Maintainer: Angelo M. Mineo

Diff between normalp versions 0.6.8 dated 2009-01-27 and 0.6.9 dated 2012-09-03

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New package pbdMPI with initial version 0.1-0
Package: pbdMPI
Version: 0.1-0
Date: 2012-08-24
Title: Programming with Big Data -- Interface to MPI
Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email = "wccsnow@gmail.com"), person("George", "Ostrouchov", role = "aut"), person("Drew", "Schmidt", role = "aut"), person("Pragneshkumar", "Patel", role = "aut"), person("Hao", "Yu", role = "aut"))
Depends: R (>= 2.13.0), methods
LazyLoad: yes
LazyData: yes
Description: pbdMPI provides an efficient interface to MPI by utilizing S4 classes and methods with a focus on Single Program/Multiple Data (SPMD) parallel programming style, which is intended for batch parallel execution.
SystemRequirements: OpenMPI (>= 1.5.4) on Linux and Mac, MPICH2 (>= 1.4.1p1) on Windows
License: GPL (>= 2)
URL: http://r-pbd.org/
Packaged: 2012-09-02 17:05:50 UTC; snoweye
Author: Wei-Chen Chen [aut, cre], George Ostrouchov [aut], Drew Schmidt [aut], Pragneshkumar Patel [aut], Hao Yu [aut]
Maintainer: Wei-Chen Chen
Repository: CRAN
Date/Publication: 2012-09-03 10:03:01

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Package quantreg updated to version 4.85 with previous version 4.81 dated 2012-06-25

Title: Quantile Regression
Description: Quantile regression and related methods.
Author: Roger Koenker
Maintainer: Roger Koenker

Diff between quantreg versions 4.81 dated 2012-06-25 and 4.85 dated 2012-09-03

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Package gcmr updated to version 0.5.0 with previous version 0.4 dated 2012-08-08

Title: Gaussian Copula Marginal Regression
Description: likelihood inference in Gaussian copula marginal regression models
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin

Diff between gcmr versions 0.4 dated 2012-08-08 and 0.5.0 dated 2012-09-03

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Package VennDiagram updated to version 1.5.1 with previous version 1.2.1 dated 2012-06-06

Title: Generate high-resolution Venn and Euler plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros

Diff between VennDiagram versions 1.2.1 dated 2012-06-06 and 1.5.1 dated 2012-09-03

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Package tau updated to version 0.0-15 with previous version 0.0-14 dated 2012-08-27

Title: Text Analysis Utilities
Description: Utilities for text analysis
Author: Christian Buchta [aut], Kurt Hornik [aut, cre], Ingo Feinerer [aut], David Meyer [aut]
Maintainer: Kurt Hornik

Diff between tau versions 0.0-14 dated 2012-08-27 and 0.0-15 dated 2012-09-03

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Package StatDA updated to version 1.6.3 with previous version 1.6.2 dated 2012-01-03

Title: Statistical Analysis for Environmental Data
Description: This package offers different possibilities to make statistical analysis for Environmental Data.
Author: Peter Filzmoser
Maintainer: Peter Filzmoser

Diff between StatDA versions 1.6.2 dated 2012-01-03 and 1.6.3 dated 2012-09-03

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Package slam updated to version 0.1-25 with previous version 0.1-24 dated 2012-06-13

Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik, David Meyer, Christian Buchta
Maintainer: Kurt Hornik

Diff between slam versions 0.1-24 dated 2012-06-13 and 0.1-25 dated 2012-09-03

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Package norm updated to version 1.0-9.4 with previous version 1.0-9.3 dated 2012-09-02

Title: Analysis of multivariate normal datasets with missing values
Description: Analysis of multivariate normal datasets with missing values
Author: Ported to R by Alvaro A. Novo . Original by Joseph L. Schafer .
Maintainer: John Fox

Diff between norm versions 1.0-9.3 dated 2012-09-02 and 1.0-9.4 dated 2012-09-03

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Package cba updated to version 0.2-10 with previous version 0.2-9 dated 2012-01-15

Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta

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Package arulesSequences updated to version 0.2-2 with previous version 0.2-1 dated 2012-01-24

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, with contributions from Daniel Diaz
Maintainer: Christian Buchta

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Package arules updated to version 1.0-10 with previous version 1.0-9 dated 2012-08-22

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

Diff between arules versions 1.0-9 dated 2012-08-22 and 1.0-10 dated 2012-09-03

 arules-1.0-10/arules/DESCRIPTION         |   10 ++++++----
 arules-1.0-10/arules/MD5                 |   20 ++++++++++----------
 arules-1.0-10/arules/NAMESPACE           |   14 ++++++++++++--
 arules-1.0-10/arules/data/Adult.rda      |binary
 arules-1.0-10/arules/data/AdultUCI.rda   |binary
 arules-1.0-10/arules/data/Epub.rda       |binary
 arules-1.0-10/arules/data/Groceries.rda  |binary
 arules-1.0-10/arules/data/Income.rda     |binary
 arules-1.0-10/arules/data/IncomeESL.rda  |binary
 arules-1.0-10/arules/inst/NEWS           |only
 arules-1.0-10/arules/inst/doc/arules.pdf |binary
 arules-1.0-9/arules/CHANGES              |only
 12 files changed, 28 insertions(+), 16 deletions(-)

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Package MBESS updated to version 3.3.2 with previous version 3.2.1 dated 2011-05-09

Title: MBESS
Description: MBESS implements methods that are especially useful to researchers working within the behavioral, educational, and social sciences (both substantive researchers and methodologists), Many of the methods contained within MBESS are applicable to quantitative research in general,
Author: Ken Kelley and Keke Lai
Maintainer: Keke Lai

Diff between MBESS versions 3.2.1 dated 2011-05-09 and 3.3.2 dated 2012-09-03

 DESCRIPTION                   |   12 
 MD5                           |only
 R/CFA.1.R                     |  155 +++++--
 R/ci.cv.R                     |  246 ++++++------
 R/ci.pvaf.R                   |   91 ++--
 R/ci.reliability.R            |  851 ++++++++++++++++++++++++------------------
 R/ci.reliability.bs.R         |    8 
 R/cor2cov.R                   |   26 -
 R/mediation.R                 |  519 ++++++++++++-------------
 R/mediation.effect.bar.plot.R |    4 
 R/mediation.effect.plot.R     |    4 
 R/ss.aipe.reliability.R       |  730 +++++++++++++++++-------------------
 R/ss.aipe.sem.path.R          |    2 
 R/ss.aipe.sem.path.sensitiv.R |    4 
 R/vit.R                       |    2 
 R/vit.fitted.R                |    2 
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 data/Gardner.LD.rda           |binary
 man/CFA.1.Rd                  |   27 -
 man/MBESS-package.Rd          |    8 
 man/ci.pvaf.Rd                |  128 +++---
 man/ci.reliability.Rd         |  131 ++++--
 man/ci.reliability.bs.Rd      |   74 +--
 man/ci.src.Rd                 |    6 
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 man/likCIESCRD.Rd             |only
 man/mediation.Rd              |   81 +++
 man/ss.aipe.reliability.Rd    |  177 ++++----
 man/ssAIPECRD.Rd              |only
 man/ssAIPECRDES.Rd            |only
 man/wideFormat.Rd             |only
 34 files changed, 1815 insertions(+), 1473 deletions(-)

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Package Ckmeans.1d.dp updated to version 2.4 with previous version 2.3 dated 2012-08-28

Title: Optimal distance-based clustering for one-dimensional data
Description: This package contains a function to cluster one-dimensional data optimally using dynamic programming to minimize the sum of squares of within cluster distances. It provides an alternative to the heuristic k-means algorithm which does not guarantee optimality.
Author: Joe Song and Haizhou Wang
Maintainer: Haizhou Wang

Diff between Ckmeans.1d.dp versions 2.3 dated 2012-08-28 and 2.4 dated 2012-09-03

 DESCRIPTION                |    8 ++++----
 MD5                        |    9 +++++----
 NAMESPACE                  |    3 ++-
 R/Ckmeans.1d.dp.R          |    5 ++---
 man/Ckmeans.1d.dp.Rd       |   22 +++++++++++-----------
 man/print.Ckmeans.1d.dp.Rd |only
 6 files changed, 24 insertions(+), 23 deletions(-)

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