Mon, 24 Jun 2013

Package TestScorer updated to version 1.2 with previous version 1.1-0 dated 2013-04-19

Title: GUI for obtaining raw & transformed tests scores. Saves results in tabular format.
Description: GUI for entering tests items and obtaining raw and transformed scores. The results are shown in the console and can be saved to a text file for further statistical analysis. The GUI also generates scripts for scoring tests defined by the user.
Author: Manel Salamero
Maintainer: Manel Salamero

Diff between TestScorer versions 1.1-0 dated 2013-04-19 and 1.2 dated 2013-06-24

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Package eha updated to version 2.2-6 with previous version 2.2-5 dated 2013-05-13

Title: Event History Analysis
Description: Event history analysis: Sampling of risk sets in Cox regression, selections in the Lexis diagram, bootstrapping. Parametric proportional hazards fitting with left truncation and right censoring for common families of distributions, piecewise constant hazards, and discrete models. AFT regression for left truncated and right censored data. Binary and Poisson regression for clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström
Maintainer: Göran Broström

Diff between eha versions 2.2-5 dated 2013-05-13 and 2.2-6 dated 2013-06-24

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New package tsModel with initial version 0.6
Package: tsModel
Title: Time Series Modeling for Air Pollution and Health
Depends: R (>= 3.0.0)
Imports: splines, stats
Suggests: gam
Date: 2013-06-24
Version: 0.6
Author: Roger D. Peng , with contributions from Aidan McDermott
Maintainer: Roger D. Peng
Description: Tools for specifying time series regression models
License: GPL (>= 2)
Packaged: 2013-06-24 19:20:01 UTC; rdpeng
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 23:00:11

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Package QZ updated to version 0.1-2 with previous version 0.1-1 dated 2013-06-04

Title: Generalized Eigenvalues and QZ Decomposition
Description: QZ package provides generalized eigenvalues and QZ decomposition (generalized Schur form) for an N-by-N non-symmetric matrix A or paired matrices (A,B) with eigenvalues reordering mechanism. The package is mainly based complex*16 and double precision of LAPACK library (version 3.4.2.)
Author: Wei-Chen Chen, partly adapted and using routines from LAPACK.
Maintainer: Wei-Chen Chen

Diff between QZ versions 0.1-1 dated 2013-06-04 and 0.1-2 dated 2013-06-24

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Package pmr updated to version 1.2.1 with previous version 1.2.0 dated 2013-05-20

Title: Probability Models for Ranking Data
Description: Descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce models, distance-based models, and rank-ordered logit models) and visualization with multidimensional preference analysis for ranking data are provided. Current, only complete rankings are supported by this package.
Author: Paul H. Lee and Philip L. H. Yu
Maintainer: Paul H. Lee

Diff between pmr versions 1.2.0 dated 2013-05-20 and 1.2.1 dated 2013-06-24

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Package GSIF updated to version 0.3-3 with previous version 0.3-2 dated 2013-04-24

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [aut], Gerard Heuvelink [aut], Brendan Malone [ctb], Hannes Reuter [ctb]
Maintainer: Tomislav Hengl

Diff between GSIF versions 0.3-2 dated 2013-04-24 and 0.3-3 dated 2013-06-24

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Package CoClust updated to version 0.2-9 with previous version 0.2-7 dated 2012-08-05

Title: Copula based cluster analysis
Description: Copula based cluster analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini

Diff between CoClust versions 0.2-7 dated 2012-08-05 and 0.2-9 dated 2013-06-24

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Package wethepeople updated to version 0.6.1 with previous version 0.5 dated 2013-06-04

Title: An R client for interacting with the White House's "We The People" petition API.
Description: Implements an R client for the We The People petitions API. The client supports loading petitions, signatures, and users. Additionally, the package includes petition and signature data samples. There are also several functions for analyzing and visualizing the data. Term frequency calculations and word clouds are supported using the tm and wordcloud package, respectively. Petition and issue summary plots are also implemented using the ggplot2 package. For additional information about the We The People project, see Note that the API limits requests to 10/second. For bulk data loading, please use the data dump provided by the White House:
Author: Yoni Ben-Meshulam
Maintainer: Yoni Ben-Meshulam

Diff between wethepeople versions 0.5 dated 2013-06-04 and 0.6.1 dated 2013-06-24

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Package LiblineaR updated to version 1.80-7 with previous version 1.80-6 dated 2013-03-26

Title: Linear Predictive Models Based On The Liblinear C/C++ Library.
Description: This R package is a wrapper around the liblinear C/C++ library for machine learning. LIBLINEAR is a linear classifier for data with millions of instances and features. It supports L2-regularized classifiers (such as L2-loss linear SVM, L1-loss linear SVM, and logistic regression) as well as L1-regularized classifiers (such as L2-loss linear SVM and logistic regression). The main features of LiblineaR include multi-class classification (one-vs-the rest, and Crammer & Singer method), cross validation for model selection, probability estimates (logistic regression only) or weights for unbalanced data. The estimation of the models is particularly fast as compared to other libraries. For more information on the C/C++ liblinear library itself, refer to R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin. LIBLINEAR: A Library for Large Linear Classification, Journal of Machine Learning Research 9(2008), 1871-1874, available at . The two first blocks of the package version indicates which version of liblinear is currently supported. For example: 1.32-14 means that the package supports the version 1.32 of liblinear.
Author: Thibault Helleputte
Maintainer: Thibault Helleputte

Diff between LiblineaR versions 1.80-6 dated 2013-03-26 and 1.80-7 dated 2013-06-24

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New package equateIRT with initial version 1.0
Package: equateIRT
Type: Package
Title: Direct, chain and average equating coefficients with standard errors using IRT methods.
Imports: statmod
Version: 1.0
Date: 2013-06-24
Author: Michela Battauz
Maintainer: Michela Battauz
Description: This package computes direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items.
License: GPL (>= 2)
Packaged: 2013-06-24 15:22:59 UTC; Michela
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 17:42:50

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New package decctools with initial version 0.1.0
Package: decctools
Type: Package
Author: James Keirstead
Maintainer: James Keirstead
Version: 0.1.0
License: GPL-2
Title: Get energy data from the UK Dept of Energy and Climate Change
Description: decctools provides functions for retrieving energy statistics from the United Kingdom Department of Energy and Climate Change and related data sources. The current version focuses on total final energy consumption statistics at the local authority, MSOA, and LSOA geographies. Methods for calculating the generation mix of grid electricity and its associated carbon intensity are also provided.
Date: 2013-04-14
Depends: stringr, XLConnect, XML, lubridate, reshape2, RCurl, plyr
LazyData: true
Collate: 'decctools.r' 'utils.r' 'msoa.r' 'lsoa.r' 'lad.r' 'carbon-intensity.r'
Packaged: 2013-06-24 14:54:06 UTC; admin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 17:21:40

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Package xts updated to version 0.9-5 with previous version 0.9-4 dated 2013-06-09

Title: eXtensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Author: Jeffrey A. Ryan, Joshua M. Ulrich
Maintainer: Jeffrey A. Ryan

Diff between xts versions 0.9-4 dated 2013-06-09 and 0.9-5 dated 2013-06-24

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Package Rcpp updated to version 0.10.4 with previous version 0.10.3 dated 2013-03-23

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library which facilitate the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Rcpp attributes provide a high-level syntax for declaring C++ functions as callable from R and automatically generating the code required to invoke them. Attributes are intended to facilitate both interactive use of C++ within R sessions as well as to support R package development. Attributes are built on top of Rcpp modules and their implementation is based on previous work in the inline package. Many examples are included, and around 881 unit tests in 412 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development should always use this Rcpp package instead. Additional documentation is available via the paper by Eddelbuettel and Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.10.3 dated 2013-03-23 and 0.10.4 dated 2013-06-24

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 man/pluginsAttribute.Rd                                       |    3 
 man/setRcppClass.Rd                                           |    6 
 src/Date.cpp                                                  |    6 
 src/Makevars                                                  |    6 
 src/Module.cpp                                                |    4 
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New package enviPat with initial version 1.0
Package: enviPat
Type: Package
Title: Isotope pattern, profile and centroid calculation.
Version: 1.0
Date: 2013-03-06
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos
Description: Fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.
License: GPL-2
Packaged: 2013-06-24 14:19:04 UTC; loosmart
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-24 16:27:55

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New package TapeR with initial version 0.3.0
Package: TapeR
Type: Package
Title: Flexible tree taper curves based on Semiparametric Mixed Models.
Version: 0.3.0
Date: 2013-06-24
Authors@R: c(person(given = "Edgar", family = "Kublin", role = "aut"), person(given = "Johannes", family = "Breidenbach", role = c("ctb","cre"), email = ""))
Author: Edgar Kublin
Maintainer: Johannes Breidenbach,
Description: This package implements functions for fitting taper curves (a semiparametric linear mixed effects taper model) to diameter measurements along stems. Further functions are provided to estimate the uncertainty around the predicted curves, to calculate timber volume (also by sections) and marginal (e.g., upper) diameters. Uncertainties of single tree volume predictions resulting from uncertainties in the taper equations tree height models (tariffs) are provided. The example data include the taper curve parameters for Norway spruce used in the 3rd German NFI fitted to 380 trees and a subset of section-wise diameter measurements of these trees. The functions implemented here are detailed in the following publication: Kublin, E., Breidenbach, J., Kaendler, G. (2013) A flexible stem taper and volume prediction method based on mixed-effects B-spline regression, Eur J For Res, accepted with minor revisions (11 June 2013).
License: GPL (>= 2)
LazyLoad: yes
Depends: nlme, splines, pracma
Packaged: 2013-06-24 08:27:24 UTC; JOB
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 10:58:31

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New package netweavers with initial version 1.0
Package: netweavers
Type: Package
Title: NetWeAvers: Weighted Averages for Networks
Version: 1.0
Date: 2013-04-04
Author: Elizabeth McClellan
Maintainer: Elizabeth McClellan
Description: This package summarizes quantified peptide data, fits linear models on and performs network analysis for proteomics mass spectrometry data.
Depends: R (>= 2.10), BiocGenerics, Biobase, igraph, limma
License: GPL-2
LazyLoad: yes
Packaged: 2013-06-24 07:12:32 UTC; Elizabeth
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 10:20:41

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Package reporttools updated to version 1.0.9 with previous version 1.0.8 dated 2012-03-23

Title: Generate LaTeX tables of descriptive statistics
Description: The functions in this package are especially helpful when writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach

Diff between reporttools versions 1.0.8 dated 2012-03-23 and 1.0.9 dated 2013-06-24

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New package d3Network with initial version 0.2
Package: d3Network
Title: Tools for creating D3 JavaScript directed network graphs from R
Description: This packages is intended to make it easy to create D3 JavaScript directed network graphs from R using data frames.
Version: 0.2
Date: 2013-06-20
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
License: GPL (>= 2)
Depends: R (>= 2.1.5)
Imports: plyr, rjson, whisker
Collate: 'd3SimpleNetwork.R' 'd3ForceNetwork.R' 'd3Network.R' 'templates.R' 'utils.R'
Packaged: 2013-06-24 00:25:07 UTC; christophergandrud
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 08:21:20

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New package BioGeoBEARS with initial version 0.1.1
Package: BioGeoBEARS
Type: Package
Title: BioGeography with Bayesian (and likelihood) Evolutionary Analysis in R Scripts
Version: 0.1.1
Date: 2013-06-23
Authors@R: c(person("Nicholas J.", "Matzke", email = "", role = c("aut", "cre", "cph")))
Maintainer: Nicholas J. Matzke
Depends: rexpokit, cladoRcpp, optimx, FD, ape, methods, parallel, compiler, LaplacesDemon, phylobase
LinkingTo: ape
Suggests: xtable
Description: BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss along a phylogenetic branch). LAGRANGE also has a fixed cladogenic model which gives equal probability to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new species starts in a subset of the ancestral range, (3) the ancestral range is copied to both species; in all cases, at least one species must have a starting range of size 1. LAGRANGE assigns equal probability to each of these events, and zero probability to other events. BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. The relative probability of different descendent range sizes is also parameterized and thus can also be specified or estimated. The flexibility available in BioGeoBEARS also enables the natural incorporation of (1) imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil geographic range data, when the fossils are tips on the phylogeny.
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: true
Packaged: 2013-06-24 02:21:00 UTC; nickm
Author: Nicholas J. Matzke [aut, cre, cph]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 08:13:17

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