Tue, 25 Sep 2012

Package survey updated to version 3.29 with previous version 3.28-2 dated 2012-07-03

Title: analysis of complex survey samples
Description: Summary statistics, two-sample tests, 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

Diff between survey versions 3.28-2 dated 2012-07-03 and 3.29 dated 2012-09-25

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Package clinfun updated to version 1.0.2 with previous version 1.0.1 dated 2012-08-14

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

Diff between clinfun versions 1.0.1 dated 2012-08-14 and 1.0.2 dated 2012-09-25

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New package ccChooser with initial version 0.2.6
Package: ccChooser
Type: Package
Title: Developing a core collections
Version: 0.2.6
Date: 2012-09-25
Author: Marcin Studnicki and Konrad Debski
Maintainer: Marcin Studnicki
Depends: R(>= 2.14.1), cluster (>= 1.13.1)
Description: ccChooser can be used to developing and evaluation of core collections for germplasm collections (entire collection). This package used to develop a core collection for biological resources like genbanks. A core collection is defined as a sample of accessions that represent, with the lowest possible level of redundancy, the genetic diversity (the richness of gene or genotype categories) of the entire collection. The establishing a core collection that represents genetic diversity of the entire collection with minimum loss of its original diversity and minimum redundancies is an important problem for gene-banks curators and crop breeders. ccChooser establish core collection base on phenotypic data (agronomic, morphological, phenological).
License: GPL (>= 2)
Packaged: 2012-09-25 20:10:59 UTC; Marcin
Repository: CRAN
Date/Publication: 2012-09-26 03:01:39

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Package BaSTA updated to version 1.4 with previous version 1.3 dated 2012-07-13

Title: A package for estimating age-specific survival from incomplete capture-recapture/recovery data
Description: This package estimates survival and mortality with covariates from capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots.
Author: Fernando Colchero, Owen Jones, Maren Rebke
Maintainer: Fernando Colchero

Diff between BaSTA versions 1.3 dated 2012-07-13 and 1.4 dated 2012-09-25

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New package svapls with initial version 1.0
Package: svapls
Type: Package
Title: Surrogate variable analysis using partial least squares in a gene expression study.
Version: 1.0
Date: 2012-07-23
Author: Sutirtha Chakraborty, Somnath Datta and Susmita Datta
Maintainer: Sutirtha Chakraborty
Depends: R (>= 2.0), class, stats, pls
Description: Accurate identification of genes that are truly differentially expressed over two sample varieties, after adjusting for hidden subject-specific effects of residual heterogeneity.
License: GPL-3
Collate: fitModel.R svpls.R hfp.R
Packaged: 2012-09-24 20:28:43 UTC; SUTIRTHA
Repository: CRAN
Date/Publication: 2012-09-25 17:07:59

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Package RcppArmadillo updated to version 0.3.4.2 with previous version 0.3.4.1 dated 2012-09-18

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 3.4.2). 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. Armadillo is licensed under the GNU LGPL version 3 or later, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.3.4.1 dated 2012-09-18 and 0.3.4.2 dated 2012-09-25

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Package isva updated to version 1.7 with previous version 1.6 dated 2012-09-25

Title: Independent Surrogate Variable Analysis
Description: Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors.
Author: Andrew E Teschendorff
Maintainer:

Diff between isva versions 1.6 dated 2012-09-25 and 1.7 dated 2012-09-25

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Package gRbase updated to version 1.6-3 with previous version 1.6-2 dated 2012-08-06

Title: A package for graphical modelling in R
Description: The gRbase package provides certain general constructs which are used by other graphical modelling packages, in particular by the packages gRain, gRim and gRc. gRbase contains several datasets relevant for use in connection with graphical models. Almost all datasets used in the book Graphical Models with R (2012) are contained in gRbase. gRbase implements several graph algorithms (based mainly on representing graphs as adjacency matrices - either in the form of a standard matrix or a sparse matrix). Some graph algorithms are: * maximum cardinality search (for marked and unmarked graphs). * moralize * triangulate * junctionTree gRbase facilities for array operations, gRbase implements functions for testing for conditional independence. gRbase illustrates how hierarchical log-linear models (hllm) may be implemented and describes concept of gmData (graphical meta data). These features, however, are not maintained anymore and remains in gRbase only because there exists a paper describing these facilities: A Common Platform for Graphical Models in R: The gRbase Package, Journal of Statistical Software, Vol 14, No 17, 2005.
Author: S°ren H°jsgaard with contributions from Claus Dethlefsen and Clive Bowsher
Maintainer: S°ren H°jsgaard

Diff between gRbase versions 1.6-2 dated 2012-08-06 and 1.6-3 dated 2012-09-25

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Package timetools updated to version 1.1-3 with previous version 1.1-2 dated 2012-04-25

Title: provides objects and tools to manipulate irregular unhomogeneous time data and subtime data.
Description: This package is intended to manipulate irregular time series such as subtime series, series based on time intervals, etc. This package uses only POSIX* format. Main things defined in this package are the classes POSIXcti, POSIXctp, TimeIntervalDataFrame, TimeInstantDataFrame, SubtimeDataFrame, methods to switch from one class to another and the changeSupport method for TimeIntervalDataFrame.
Author: Vladislav Navel
Maintainer: Vladislav Navel

Diff between timetools versions 1.1-2 dated 2012-04-25 and 1.1-3 dated 2012-09-25

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Package seriation updated to version 1.0-7 with previous version 1.0-6 dated 2011-10-19

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 1.0-6 dated 2011-10-19 and 1.0-7 dated 2012-09-25

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Package PearsonDS updated to version 0.94 with previous version 0.93 dated 2012-04-02

Title: Pearson Distribution System
Description: Implementation of the Pearson distribution system, including full support for the (d,p,q,r)-family of functions for probability distributions and fitting via method of moments and maximum likelihood method.
Author: Martin Becker and Stefan Kl÷▀ner
Maintainer: Martin Becker

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Package spdep updated to version 0.5-51 with previous version 0.5-50 dated 2012-08-31

Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assun├ž├úo/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.
Author: Roger Bivand , with contributions by Micah Altman, Luc Anselin, Renato Assun├ž├úo, Olaf Berke, Andrew Bernat, Guillaume Blanchet, Eric Blankmeyer, Marilia Carvalho, Bjarke Christensen, Yongwan Chun, Carsten Dormann, St├ęphane Dray, Rein Halbersma, Elias Krainski, Pierre Legendre, Nicholas Lewin-Koh, Hongfei Li, Jielai Ma, Giovanni Millo, Werner Mueller, Hisaji Ono, Pedro Peres-Neto, Gianfranco Piras, Markus Reder, Michael Tiefelsdorf, and Danlin Yu.
Maintainer: Roger Bivand

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Package smoothSurv updated to version 1.1 with previous version 1.0 dated 2012-01-07

Title: Survival Regression with Smoothed Error Distribution
Description: This package contains primarily a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Libary Version 0.3.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek

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Package mixAK updated to version 2.6 with previous version 2.4 dated 2012-06-19

Title: Mixture of methods including mixtures
Description: This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures
Author: Arnošt Komárek
Maintainer: Arnošt Komárek

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Package emoa updated to version 0.5-0 with previous version 0.4-8 dated 2011-10-18

Title: Evolutionary Multiobjective Optimization Algorithms
Description: Collection of building blocks for the design and analysis of evolutionary multiobjective optimization algorithms.
Author: Olaf Mersmann
Maintainer: Olaf Mersmann

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Package rgdal updated to version 0.7-19 with previous version 0.7-18 dated 2012-08-30

Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.0) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Timothy H. Keitt , Roger Bivand , Edzer Pebesma , Barry Rowlingson
Maintainer: Roger Bivand

Diff between rgdal versions 0.7-18 dated 2012-08-30 and 0.7-19 dated 2012-09-25

 ChangeLog      | 1184 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 DESCRIPTION    |    8 
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Package spacetime updated to version 0.8-0 with previous version 0.7-1 dated 2012-07-04

Title: classes and methods for spatio-temporal data
Description: A package with classes and methods for spatio-temporal data. In particular, space-time regular lattices, sparse lattices, irregular data, and simple trajectories are supported. Utility functions are provided for plotting data as map sequences (lattice or animation) or multiple time series; for spatial and temporal selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedict Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma

Diff between spacetime versions 0.7-1 dated 2012-07-04 and 0.8-0 dated 2012-09-25

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Package qpcR updated to version 1.3-7 with previous version 1.3-6 dated 2012-02-22

Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).
Author: Andrej-Nikolai Spiess
Maintainer: Andrej-Nikolai Spiess

Diff between qpcR versions 1.3-6 dated 2012-02-22 and 1.3-7 dated 2012-09-25

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Package rfPermute updated to version 1.5 with previous version 1.4 dated 2012-09-21

Title: Estimate permutation p-values for importance metrics.
Description: Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed.
Author: Eric Archer
Maintainer: Eric Archer

Diff between rfPermute versions 1.4 dated 2012-09-21 and 1.5 dated 2012-09-25

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New package lpint with initial version 1.0
Package: lpint
Type: Package
Title: Local polynomial esitmators of intensity function or its derivatives
Version: 1.0
Date: 2012-09-21
Author: Feng Chen
Maintainer: Feng Chen
Description: Estimates the intensity function or its derivative of a give a given order using the local polynomial method
License: GPL (>= 2.0)
LazyLoad: yes
Packaged: 2012-09-25 04:38:52 UTC; z3243864
Repository: CRAN
Date/Publication: 2012-09-25 06:02:02

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Package isva updated to version 1.6 with previous version 1.5 dated 2012-09-24

Title: Independent Surrogate Variable Analysis
Description: Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors.
Author: Andrew E Teschendorff
Maintainer:

Diff between isva versions 1.5 dated 2012-09-24 and 1.6 dated 2012-09-25

 DESCRIPTION         |    8 ++++----
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 4 files changed, 13 insertions(+), 11 deletions(-)

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New package eeptools with initial version 0.1
Package: eeptools
Type: Package
Title: Convenience functions for education data
Version: 0.1
Date: 2012-07-21
Author: Jared E. Knowles
Maintainer: Jared E. Knowles
Description: Free and open source software to make education evaluation easier.Shortcuts and utilities to make R easier to use in an educational evaluation office.
License: GPL-3
Depends: R (>= 2.15.1), stringr, ggplot2, plyr, proto, grid, maps,mapproj
Suggests: reshape
Packaged: 2012-09-24 23:20:55 UTC; Jared
Repository: CRAN
Date/Publication: 2012-09-25 06:00:05

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Package BCBCSF updated to version 0.0-2 with previous version 0.0-1 dated 2011-09-14

Title: Bias-corrected Bayesian Classification with Selected Features
Description: This software is used to predict the discrete class labels based on a selected subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.
Author: Longhai Li
Maintainer: Longhai Li

Diff between BCBCSF versions 0.0-1 dated 2011-09-14 and 0.0-2 dated 2012-09-25

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Package descr updated to version 0.9.9 with previous version 0.9.8 dated 2012-08-07

Title: Descriptive statistics
Description: This package contains functions to describe weighted categorical variables and functions to facilitate the character encoding conversion of objects.
Author: Jakson Aquino. Includes R source code and/or documentation written by Dirk Enzmann, Marc Schwartz, and Nitin Jain
Maintainer: Jakson Aquino

Diff between descr versions 0.9.8 dated 2012-08-07 and 0.9.9 dated 2012-09-25

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