Mon, 20 Apr 2015

Package crunch updated to version 1.1.1 with previous version 1.1.0 dated 2015-04-16

Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson

Diff between crunch versions 1.1.0 dated 2015-04-16 and 1.1.1 dated 2015-04-20

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More information about crunch at CRAN
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New package xml2 with initial version 0.1.0
Package: xml2
Version: 0.1.0
Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre")), person("Jeroen", "Ooms", role = "ctb"), person("RStudio", role = "cph"), person("R Foundation", role = "ctb", comment = "Copy of R-project homepage cached as example") )
Depends: R (>= 3.1.0)
Imports: Rcpp
LinkingTo: Rcpp (>= 0.11.4.6), BH
Suggests: testthat, curl
License: GPL (>= 2)
Packaged: 2015-04-20 19:36:32 UTC; hadley
Author: Hadley Wickham [aut, cre], Jeroen Ooms [ctb], RStudio [cph], R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-20 22:43:45

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Package weirs updated to version 0.24 with previous version 0.23 dated 2013-12-03

Title: A Hydraulics Package to Compute Open-Channel Flow over Weirs
Description: This hydraulics package provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Author: William Asquith
Maintainer: William Asquith

Diff between weirs versions 0.23 dated 2013-12-03 and 0.24 dated 2015-04-20

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Package solaR updated to version 0.41 with previous version 0.38 dated 2014-04-27

Title: Radiation and Photovoltaic Systems
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpiñán Lamigueiro
Maintainer: Oscar Perpiñán Lamigueiro

Diff between solaR versions 0.38 dated 2014-04-27 and 0.41 dated 2015-04-20

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Package prevalence updated to version 0.4.0 with previous version 0.3.0 dated 2014-10-21

Title: Tools for Prevalence Assessment Studies
Description: The prevalence package provides Frequentist and Bayesian methods for prevalence assessment studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from http://mcmc-jags.sourceforge.net/.
Author: Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut], Johannes Charlier [aut], Bruno Levecke [aut], Nicolas Praet [aut], Sophie Roelandt [aut], Suzanne Smit [aut], Pierre Dorny [aut], Dirk Berkvens [aut], Niko Speybroeck [aut]
Maintainer: Brecht Devleesschauwer

Diff between prevalence versions 0.3.0 dated 2014-10-21 and 0.4.0 dated 2015-04-20

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New package RSocrata with initial version 1.6.0-12
Package: RSocrata
Title: Download 'Socrata' Data Sets as R Data Frames
Description: Provides easier interaction with Socrata open data portals \url{http://dev.socrata.com}. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format. Manages throttling by 'Socrata'.
Version: 1.6.0-12
Date: 2015-4-20
URL: https://github.com/Chicago/RSocrata
BugReports: https://github.com/Chicago/RSocrata/issues
Depends: httr (>= 0.3), jsonlite (>= 0.9.14), mime (>= 0.2)
Imports: curl (>= 0.5)
Suggests: RUnit
Author: Hugh Devlin, Ph. D. and Tom Schenk, Jr.
Maintainer: "Tom Schenk Jr."
License: MIT + file LICENSE
Packaged: 2015-04-20 17:03:19 UTC; 362222
NeedsCompilation: no
X-CRAN-Comment: Archived on 2014-12-07 as maintainer address bounced.
Repository: CRAN
Date/Publication: 2015-04-20 22:13:33

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Package carcass updated to version 1.4 with previous version 1.3 dated 2014-10-02

Title: Estimation of the Number of Fatalities from Carcass Searches
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt, Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner, Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp
Maintainer: Fraenzi Korner-Nievergelt

Diff between carcass versions 1.3 dated 2014-10-02 and 1.4 dated 2015-04-20

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Package TestScorer updated to version 1.7 with previous version 1.6 dated 2014-07-05

Title: GUI for Entering Test Items and Obtaining Raw and Transformed Scores
Description: GUI for entering test items and obtaining raw and transformed scores. The results are shown on the console and can be saved to a tabular text file for further statistical analysis. The user can define his own tests and scoring procedures through a GUI.
Author: Manel Salamero
Maintainer: Manel Salamero

Diff between TestScorer versions 1.6 dated 2014-07-05 and 1.7 dated 2015-04-20

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Package sparkTable updated to version 1.0.0 with previous version 0.12.0 dated 2014-11-17

Title: Sparklines and Graphical Tables for TeX and HTML
Description: Create sparklines and graphical tables for documents and websites.
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik

Diff between sparkTable versions 0.12.0 dated 2014-11-17 and 1.0.0 dated 2015-04-20

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New package rLiDAR with initial version 0.1
Package: rLiDAR
Type: Package
Title: LiDAR Data Processing and Visualization
Version: 0.1
Author: Carlos A. Silva, Nicholas L. Crookston, Andrew T. Hudak, Lee A. Vierling
Maintainer: Carlos A. Silva
Depends: R (>= 3.1.2)
Imports: spatstat,sp,deldir,plyr,raster,geometry,rgl,bitops
Description: Set of tools for reading, processing and visualizing small set of LiDAR (Light Detection and Ranging) data for forest inventory applications.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: rlidar
Repository/R-Forge/Revision: 115
Repository/R-Forge/DateTimeStamp: 2015-04-16 04:49:32
Date/Publication: 2015-04-20 17:52:06
Packaged: 2015-04-16 05:10:18 UTC; rforge
NeedsCompilation: no

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Package RANN updated to version 2.5 with previous version 2.4.1 dated 2014-07-21

Title: Fast Nearest Neighbour Search (Wraps Arya and Mount's ANN Library)
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis

Diff between RANN versions 2.4.1 dated 2014-07-21 and 2.5 dated 2015-04-20

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Package mbest updated to version 0.3 with previous version 0.1 dated 2014-06-05

Title: Moment-Based Estimation for Hierarchical Models
Description: Implements methods from the paper "Fast Moment-Based Estimation for Hierarchical Models," by Perry (2015).
Author: Patrick O. Perry
Maintainer: Patrick O. Perry

Diff between mbest versions 0.1 dated 2014-06-05 and 0.3 dated 2015-04-20

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Package fscaret updated to version 0.9.4 with previous version 0.9.3 dated 2015-03-04

Title: Automated Feature Selection from 'caret'
Description: Automated feature selection using variety of models provided by 'caret' package. This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012.
Author: Jakub Szlek [aut, cre], Aleksander Mendyk [ctb]
Maintainer: Jakub Szlek

Diff between fscaret versions 0.9.3 dated 2015-03-04 and 0.9.4 dated 2015-04-20

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Package icamix updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-29

Title: Estimation of ICA Mixture Models
Description: The icamix package provides R functions as well as a C++ library which facilitate the estimation of ICA mixture models. We have developed and implemented the NSMM-ICA algorithm that currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture models. We will continue to build in algorithms that interweave the EM step with other types of ICA techniques.
Author: Xiaotian Zhu, David R. Hunter
Maintainer: Xiaotian Zhu

Diff between icamix versions 1.0.1 dated 2014-08-29 and 1.0.2 dated 2015-04-20

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Package Frames2 updated to version 0.1.1 with previous version 0.1.0 dated 2015-01-22

Title: Estimation in Dual Frame Surveys
Description: Point and interval estimation in dual frame surveys. In contrast to classic sampling theory, where only one sampling frame is considered, dual frame methodology assumes that there are two frames available for sampling and that, overall, they cover the entire target population. Then, two probability samples (one from each frame) are drawn and information collected is suitably combined to get estimators of the parameter of interest.
Author: Antonio Arcos , Maria del Mar Rueda , Maria Giovanna Ranalli and David Molina
Maintainer: David Molina

Diff between Frames2 versions 0.1.0 dated 2015-01-22 and 0.1.1 dated 2015-04-20

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Package ABCanalysis updated to version 1.0.1 with previous version 1.0 dated 2015-02-13

Title: Computed ABC Analysis
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many").
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun

Diff between ABCanalysis versions 1.0 dated 2015-02-13 and 1.0.1 dated 2015-04-20

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Package userfriendlyscience updated to version 0.3-0 with previous version 0.2-2 dated 2015-04-07

Title: Quantitative Analysis Made Accessible
Description: Contains a number of functions that serve two goals: first, make R more accessible to people migrating from SPSS by adding a number of functions that behave roughly like their SPSS equivalents; and second, make a number of slightly more advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters

Diff between userfriendlyscience versions 0.2-2 dated 2015-04-07 and 0.3-0 dated 2015-04-20

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Package lmerTest updated to version 2.0-25 with previous version 2.0-20 dated 2014-11-21

Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented in 'lme4' package are provided. The tests comprise types I - III F tests for fixed effects, LR tests for random effects. The package also provides the calculation of population means for fixed factors with confidence intervals and corresponding plots. Finally the backward elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre], Per Bruun Brockhoff [aut, ths], Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova

Diff between lmerTest versions 2.0-20 dated 2014-11-21 and 2.0-25 dated 2015-04-20

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New package GWLelast with initial version 1.0
Package: GWLelast
Type: Package
Title: Geographically Weighted Logistic Elastic Net Regression
Version: 1.0
Date: 2015-04-20
Author: Daisuke Yoneoka, Eiko Saito
Maintainer: Daisuke Yoneoka
Description: Fit a geographically weighted logistic elastic net regression.
License: GPL-2
Suggests: testthat
Imports: doParallel,geosphere,sp,spgwr,glmnet,doMC,foreach
Packaged: 2015-04-20 03:55:57 UTC; Daisuke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-20 14:25:06

More information about GWLelast at CRAN
Permanent link

Package DNAprofiles updated to version 0.3 with previous version 0.2 dated 2014-06-23

Title: DNA Profiling Evidence Analysis
Description: Methods for studying forensic DNA profiling, in particular familial database searches.
Author: Maarten Kruijver
Maintainer: Maarten Kruijver

Diff between DNAprofiles versions 0.2 dated 2014-06-23 and 0.3 dated 2015-04-20

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More information about DNAprofiles at CRAN
Permanent link

New package ADPclust with initial version 0.6.3
Package: ADPclust
Type: Package
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast Clustering Using Adaptive Density Peak Detection). The work is built and improved upon Rodriguez and Laio[2014]'s idea. ADPclust clusters data by finding density peaks in a density-distance plot generated from local multivariate Gaussian density estimation. It includes an automatic centroids selection and parameter optimization algorithm, which finds the number of clusters and cluster centroids by comparing average silhouettes on a grid of testing clustering results; It also includes an user interactive algorithm that allows the user to manually selects cluster centroids from a two dimensional "density-distance plot".
Version: 0.6.3
Author: Yifan "Ethan" Xu , Xiao-Feng Wang
Maintainer: Yifan "Ethan" Xu
Depends: R (>= 2.14.0),
Imports: dplyr, cluster, fields, knitr
VignetteBuilder: knitr
License: GPL (>= 2)
LazyData: true
Packaged: 2015-04-20 03:40:54 UTC; yifanxu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-20 14:17:36

More information about ADPclust at CRAN
Permanent link

New package synRNASeqNet with initial version 1.0
Package: synRNASeqNet
Type: Package
Title: Synthetic RNA-Seq Network Generation and Mutual Information Estimates
Version: 1.0
Date: 2015-04-07
Author: Luciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Maintainer: Luciano Garofano
Depends: R (>= 3.1.1), parallel, parmigene, GenKern, igraph
URL: https://github.com/lucgar/synRNASeqNet
Imports: KernSmooth
Description: It implements various estimators of mutual information, such as the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, the shrinkage estimator, and the Chao-Shen estimator. It also offers wrappers to the kNN and kernel density estimators. Furthermore, it provides various index of performance evaluation such as precision, recall, FPR, F-Score, ROC-PR Curves and so on. Lastly, it provides a brand new way of generating synthetic RNA-Seq Network with known dependence structure.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2015-04-20 08:45:39 UTC; luciano
Repository: CRAN
Date/Publication: 2015-04-20 11:55:18

More information about synRNASeqNet at CRAN
Permanent link

Package RandomFieldsUtils updated to version 0.0.2 with previous version 0.0.1 dated 2015-04-09

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb]
Maintainer: Martin Schlather

Diff between RandomFieldsUtils versions 0.0.1 dated 2015-04-09 and 0.0.2 dated 2015-04-20

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Package qwraps2 updated to version 0.1.1 with previous version 0.1 dated 2015-04-08

Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into .Rnw or .Rmd files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at https://github.com/dewittpe/qwraps. The implementation and limited scope of the functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt

Diff between qwraps2 versions 0.1 dated 2015-04-08 and 0.1.1 dated 2015-04-20

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Package oro.dicom updated to version 0.5.0 with previous version 0.4.3 dated 2015-01-17

Title: Rigorous - DICOM Input / Output
Description: Data input/output functions for data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre]
Maintainer: Brandon Whitcher

Diff between oro.dicom versions 0.4.3 dated 2015-01-17 and 0.5.0 dated 2015-04-20

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Package LeafArea updated to version 0.1.0 with previous version 0.0.6 dated 2015-03-08

Title: Rapid Digital Image Analysis of Leaf Area
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi

Diff between LeafArea versions 0.0.6 dated 2015-03-08 and 0.1.0 dated 2015-04-20

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Package futile.logger updated to version 1.4.1 with previous version 1.4 dated 2015-03-21

Title: A Logging Utility for R
Description: Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe

Diff between futile.logger versions 1.4 dated 2015-03-21 and 1.4.1 dated 2015-04-20

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Package bayescount updated to version 0.9.99-5 with previous version 0.9.99-4 dated 2015-03-02

Title: Power Calculations and Bayesian Analysis of Count Distributions and FECRT Data using MCMC
Description: A set of functions to allow analysis of count data (such as faecal egg count data) using Bayesian MCMC methods. Returns information on the possible values for mean count, coefficient of variation and zero inflation (true prevalence) present in the data. A complete faecal egg count reduction test (FECRT) model is implemented, which returns inference on the true efficacy of the drug from the pre- and post-treatment data provided, using non-parametric bootstrapping as well as using Bayesian MCMC. Functions to perform power analyses for faecal egg counts (including FECRT) are also provided.
Author: Matthew Denwood [aut, cre]
Maintainer: Matthew Denwood

Diff between bayescount versions 0.9.99-4 dated 2015-03-02 and 0.9.99-5 dated 2015-04-20

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Package highlight updated to version 0.4.7 with previous version 0.4.5 dated 2015-04-15

Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
Author: Romain Francois [aut, cre], Andre Simon [ctb]
Maintainer: Romain Francois

Diff between highlight versions 0.4.5 dated 2015-04-15 and 0.4.7 dated 2015-04-20

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Package GMCM updated to version 1.2.1 with previous version 1.2 dated 2015-04-13

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau

Diff between GMCM versions 1.2 dated 2015-04-13 and 1.2.1 dated 2015-04-20

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Package gcmr updated to version 0.7.0 with previous version 0.6.1 dated 2013-07-29

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 0.6.1 dated 2013-07-29 and 0.7.0 dated 2015-04-20

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Sun, 19 Apr 2015

New package WikipediaR with initial version 1.0
Package: WikipediaR
Type: Package
Title: R-Based Wikipedia Client
Version: 1.0
Date: 2015-04-13
Authors@R: c(person("Avner", "Bar-Hen", role = c("aut", "cre"), email = "Avner.Bar-Hen@mi.parisdescartes.fr"), person("Louise", "Baschet", role = "ctb"), person("Francois-Xavier", "Jollois", role = "ctb"), person("Jeremie", "Riou", role = "ctb") )
Maintainer: Avner Bar-Hen
Description: Provides an interface to the Wikipedia web application programming interface (API), using internet connection. Three functions provide details for a specific Wikipedia page: all links that are present, all pages that link to, all the contributions (revisions for main pages, and discussions for talk pages). Two functions provide details for a specific user: all contributions, and general information (as name, gender, rights or groups). It provides additional information compared to others packages, as 'WikipediR'. It does not need login. The multiplex network that can be constructed from the results of the functions of 'WikipediaR' can be modeled as Stochastic Block Model as in Barbillon P., Donnet, S., Lazega E., and Bar-Hen A.: "Stochastic Block Models for Multiplex networks: an application to networks of researchers", ArXiv 1501.06444, http://arxiv.org/abs/1501.06444.
License: GPL (> 2)
Depends: R (>= 2.10.0), XML (>= 2.6.3)
URL: http://www.r-project.org
Repository: CRAN
Packaged: 2015-04-17 14:44:06 UTC; Louise
Author: Avner Bar-Hen [aut, cre], Louise Baschet [ctb], Francois-Xavier Jollois [ctb], Jeremie Riou [ctb]
NeedsCompilation: no
Date/Publication: 2015-04-19 22:10:18

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New package tdr with initial version 0.11
Package: tdr
Type: Package
Title: Target Diagram
Version: 0.11
Date: 2015-04-18
Encoding: UTF-8
Authors@R: person("Oscar", "Perpinan Lamigueiro", email="oscar.perpinan@gmail.com", role=c('cre', 'aut'))
Description: Implementation of target diagrams using 'lattice' and 'ggplot2' graphics. Target diagrams provide a graphical overview of the respective contributions of the unbiased RMSE and MBE to the total RMSE (Jolliff, J. et al., 2009. "Summary Diagrams for Coupled Hydrodynamic-Ecosystem Model Skill Assessment." Journal of Marine Systems 76: 64–82.)
URL: http://github.com/oscarperpinan/tdr
BugReports: https://github.com/oscarperpinan/tdr/issues
License: GPL-2
Depends: lattice, ggplot2
Imports: RColorBrewer
Suggests: latticeExtra
Packaged: 2015-04-19 08:18:13 UTC; oscar
Author: Oscar Perpinan Lamigueiro [cre, aut]
Maintainer: Oscar Perpinan Lamigueiro
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-19 22:12:15

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Package R1magic updated to version 0.3.2 with previous version 0.2 dated 2013-04-09

Title: Compressive Sampling: Sparse Signal Recovery Utilities
Description: Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple sparse signal generator, mutual cumulative coherence between two matrices and examples, Lp complex norm, scaling back regression coefficients.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen

Diff between R1magic versions 0.2 dated 2013-04-09 and 0.3.2 dated 2015-04-19

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Package BNPTSclust updated to version 1.1 with previous version 1.0 dated 2015-01-13

Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez

Diff between BNPTSclust versions 1.0 dated 2015-01-13 and 1.1 dated 2015-04-19

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Package hitandrun updated to version 0.5-1 with previous version 0.5 dated 2015-01-06

Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly from Convex Shapes
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef

Diff between hitandrun versions 0.5 dated 2015-01-06 and 0.5-1 dated 2015-04-19

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New package timeSeq with initial version 1.0.0
Package: timeSeq
Type: Package
Title: Nonparallel Differential Expressed Genes
Version: 1.0.0
Date: 2015-04-19
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao
Description: Uses a negative binomial mixed-effects (NBME) model to detect nonparallel differential expression(NPDE) genes and parallel differential expression(PDE) genes in the time course RNA-seq data.
Depends: R (>= 3.0.1)
Imports: parallel, gss, lattice, pheatmap, doParallel, foreach, reshape, edgeR
License: GPL (>= 2)
Packaged: 2015-04-19 01:56:33 UTC; gaofan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-19 07:55:48

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Package SKAT updated to version 1.0.7 with previous version 1.0.1 dated 2014-11-04

Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel regression based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee

Diff between SKAT versions 1.0.1 dated 2014-11-04 and 1.0.7 dated 2015-04-19

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New package PortfolioAnalytics with initial version 1.0.3636
Package: PortfolioAnalytics
Type: Package
Title: Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios
Authors@R: c( person(given=c("Brian","G."),family="Peterson",role=c("cre","aut","cph"), email="brian@braverock.com") , person(given="Peter",family="Carl",role=c("aut","cph"), email="peter@braverock.com") , person(given="Kris",family="Boudt",role=c("ctb","cph")) , person(given="Ross",family="Bennett",role=c("ctb","cph")) , person(given="Hezky",family="Varon",role="ctb") , person(given="Guy",family="Yollin",role="ctb") , person(given="R. Douglas",family="Martin",role="ctb") )
Version: 1.0.3636
Date: 2015-04-18
Maintainer: Brian G. Peterson
Description: Portfolio optimization and analysis routines and graphics.
Depends: R (>= 2.14.0), zoo, xts (>= 0.8), foreach, PerformanceAnalytics (>= 1.1.0)
Suggests: quantmod, DEoptim(>= 2.2.1), iterators, fGarch, Rglpk, quadprog, ROI (>= 0.1.0), ROI.plugin.glpk (>= 0.0.2), ROI.plugin.quadprog (>= 0.0.2), ROI.plugin.symphony (>= 0.0.2), pso, GenSA, corpcor, testthat, nloptr (>= 1.0.0), MASS, robustbase
License: GPL
Copyright: (c) 2004-2015
NeedsCompilation: yes
Packaged: 2015-04-19 01:37:19.121143 UTC; brian
Author: Brian G. Peterson [cre, aut, cph], Peter Carl [aut, cph], Kris Boudt [ctb, cph], Ross Bennett [ctb, cph], Hezky Varon [ctb], Guy Yollin [ctb], R. Douglas Martin [ctb]
Repository: CRAN
Date/Publication: 2015-04-19 07:38:57

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Package phonR updated to version 1.0-3 with previous version 1.0-1 dated 2015-03-05

Title: Tools for Phoneticians and Phonologists
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy

Diff between phonR versions 1.0-1 dated 2015-03-05 and 1.0-3 dated 2015-04-19

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Package mixtools updated to version 1.0.3 with previous version 1.0.2 dated 2014-05-14

Title: Tools for Analyzing Finite Mixture Models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre], Tatiana Benaglia [aut], Didier Chauveau [aut], David Hunter [aut], Ryan Elmore [ctb], Thomas Hettmansperger [ctb], Hoben Thomas [ctb], Fengjuan Xuan [ctb]
Maintainer: Derek Young

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Package gemtc updated to version 0.6-2 with previous version 0.6-1 dated 2014-12-12

Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian framework. You need either BUGS or JAGS to use this package, preferably JAGS (through the rjags package). Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef

Diff between gemtc versions 0.6-1 dated 2014-12-12 and 0.6-2 dated 2015-04-19

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Package degreenet updated to version 1.3-1 with previous version 1.3 dated 2015-04-06

Title: Models for Skewed Count Distributions Relevant to Networks
Description: Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock
Maintainer: Mark S. Handcock

Diff between degreenet versions 1.3 dated 2015-04-06 and 1.3-1 dated 2015-04-19

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Package candisc updated to version 0.6-7 with previous version 0.6-5 dated 2013-06-12

Title: Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
Description: Functions for computing and visualizing generalized canonical discriminant analyses and canonical correlation analysis for a multivariate linear model. Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA' design and is equivalent to canonical correlation analysis between a set of quantitative response variables and a set of dummy variables coded from the factor variable. The 'candisc' package generalizes this to higher-way 'MANOVA' designs for all factors in a multivariate linear model, computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D) visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly

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Package BDgraph updated to version 2.18 with previous version 2.17 dated 2015-03-10

Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

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Sat, 18 Apr 2015

Package vegdata updated to version 0.6.9 with previous version 0.6-7 dated 2014-11-01

Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (http://www.synbiosys.alterra.nl/turboveg/) and other sources (http://www.vegetweb.de). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", http://www.botanik.uni-greifswald.de/GermanSL.html).
Author: Florian Jansen
Maintainer: Florian Jansen

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New package TDCor with initial version 0.1-1
Package: TDCor
Type: Package
Title: Gene Network Inference from Time-Series Transcriptomic Data
Version: 0.1-1
Date: 2015-04-08
Author: Julien Lavenus
Maintainer: Mikael Lucas
Imports: parallel
Depends: R (>= 3.1.2), deSolve
Description: The Time-Delay Correlation algorithm (TDCor) reconstructs the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developed to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset which was used in this study is included in the package to illustrate how to use it.
License: GPL (>= 2)
Packaged: 2015-04-08 19:28:20.092 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 17:19:35

More information about TDCor at CRAN
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Package heplots updated to version 1.0-15 with previous version 1.0-12 dated 2014-07-02

Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly

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Package eHOF updated to version 1.5.8 with previous version 1.5.7 dated 2015-01-14

Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen

Diff between eHOF versions 1.5.7 dated 2015-01-14 and 1.5.8 dated 2015-04-18

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New package crimelinkage with initial version 0.0.3
Package: crimelinkage
Title: Statistical Methods for Crime Series Linkage
Version: 0.0.3
Authors@R: c( person("Michael", "Porter", email = "mporter@cba.ua.edu", role = c("aut", "cre")), person("Brian", "Reich", email = "brian_reich@ncsu.edu", role = "aut"))
Description: Statistical Methods for Crime Series Linkage. This package provides code for criminal case linkage, crime series identification, crime series clustering, and suspect identification.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
Date: 2015-04-16
BugReports:
Imports: igraph, geosphere
Suggests: fields, knitr, gbm
VignetteBuilder: knitr
Packaged: 2015-04-18 12:50:50 UTC; mdporter
Author: Michael Porter [aut, cre], Brian Reich [aut]
Maintainer: Michael Porter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 17:19:39

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Package TKF updated to version 0.0.8 with previous version 0.0.3 dated 2015-02-10

Title: Pairwise Distance Estimation with TKF91 and TKF92 Model
Description: Pairwise evolutionary distance estimation between protein sequences with the TKF91 and TKF92 model, which consider all the possible paths of transforming from one sequence to another.
Author: Ge Tan
Maintainer: Ge Tan

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Package muscle (with last version 3.8.31-4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-07-07 3.8.31-4
2014-07-04 3.8.31-3
2014-05-07 3.8.31-2
2013-03-29 3.8.31-1
2012-10-15 3.8.31-0

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Package saps (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-10-07 1.0.0

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New package plaqr with initial version 1.0
Package: plaqr
Title: Partially Linear Additive Quantile Regression
Description: Estimation, prediction, thresholding, and plotting for partially linear additive quantile regression. Intuitive functions for fitting and plotting partially linear additive quantile regression models. Uses and works with functions from the 'quantreg' package.
Version: 1.0
Authors@R: person("Adam", "Maidman", role = c("cre","aut"), email = "maidm004@umn.edu")
Maintainer: Adam Maidman
Depends: R (>= 3.0), quantreg, splines
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2015-04-18 10:59:33
Packaged: 2015-04-17 14:49:00 UTC; maidm004
Author: Adam Maidman [cre, aut]
NeedsCompilation: no

More information about plaqr at CRAN
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Package SSN updated to version 1.1.5 with previous version 1.1.4 dated 2014-11-03

Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef

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Package SSDforR updated to version 1.4.9 with previous version 1.4.8 dated 2014-12-07

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach

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Package sprex updated to version 1.1 with previous version 1.0 dated 2015-02-24

Title: Calculate Species Richness and Extrapolation Metrics
Description: Calculate species richness functions for rarefaction and extrapolation.
Author: Eric Archer
Maintainer: Eric Archer

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Package sjmisc updated to version 1.0.1 with previous version 1.0.0 dated 2015-03-22

Title: Miscellaneous Data Management Tools
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke

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More information about sjmisc at CRAN
Permanent link

New package NPC with initial version 1.0.0
Package: NPC
Type: Package
Title: Nonparametric Combination of Hypothesis Tests
Version: 1.0.0
Authors@R: person("Devin", "Caughey", email="devin.caughey@gmail.com", role=c("aut", "cre"))
Depends: R (>= 3.1.1)
LazyData: true
Description: An implementation of nonparametric combination of hypothesis tests. This package performs nonparametric combination (Pesarin and Salmaso 2010), a permutation-based procedure for jointly testing multiple hypotheses. The tests are conducted under the global "sharp" null hypothesis of no effects, and the component tests are combined on the metric of their p-values. A key feature of nonparametric combination is that it accounts for the dependence among tests under the null hypothesis. In addition to the "NPC" function, which performs nonparametric combination itself, the package also contains a number of helper functions, many of which calculate a test statistic given an input of data.
License: GPL-3
Imports: permute, dplyr, coin, matlab
Suggests: car, mvtnorm, plyr, xtable
Packaged: 2015-04-17 13:04:24 UTC; justin
Author: Devin Caughey [aut, cre]
Maintainer: Devin Caughey
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:55:51

More information about NPC at CRAN
Permanent link

Package MATA updated to version 0.3 with previous version 0.2 dated 2015-01-08

Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, which are constructed using single-model estimators and model weights.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek

Diff between MATA versions 0.2 dated 2015-01-08 and 0.3 dated 2015-04-18

 DESCRIPTION |   14 +++++++-------
 MD5         |    2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

More information about MATA at CRAN
Permanent link

Package Luminescence updated to version 0.4.3 with previous version 0.4.2 dated 2015-03-23

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Rachel K. Smedley [aut], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.4.2 dated 2015-03-23 and 0.4.3 dated 2015-04-18

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 NAMESPACE                       |    3 
 NEWS                            |  232 +++
 R/Analyse_SAR.OSLdata.R         |  415 +++---
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More information about Luminescence at CRAN
Permanent link

Package KFAS updated to version 1.1.0 with previous version 1.0.4-1 dated 2014-06-06

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: Functions for Kalman filtering, smoothing, forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske

Diff between KFAS versions 1.0.4-1 dated 2014-06-06 and 1.1.0 dated 2015-04-18

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More information about KFAS at CRAN
Permanent link

New package gbm2sas with initial version 1.0
Package: gbm2sas
Type: Package
Title: Convert GBM Object Trees to SAS Code
Version: 1.0
Date: 2015-04-10
Author: John R. Dixon
Maintainer: John R. Dixon
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
License: GPL-3
Depends: gbm
Packaged: 2015-04-16 15:33:56 UTC; i800146
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:56:14

More information about gbm2sas at CRAN
Permanent link

Package datacheck updated to version 1.2.2 with previous version 1.0.4 dated 2014-09-23

Title: Tools for Checking Data Consistency
Description: Functions to check variables against a set of data quality rules. A rule file can be accompanied by look-up tables. In addition, there are some convenience functions that may serve as an example for defining clearer 'data rules'. An HTML based user interface facilitates initial exploration of the functionality.
Author: "Simon, Reinhard (CIP)" , Jose Francisco Loff
Maintainer: "Simon, Reinhard (CIP)"

Diff between datacheck versions 1.0.4 dated 2014-09-23 and 1.2.2 dated 2015-04-18

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More information about datacheck at CRAN
Permanent link

Package daff updated to version 0.1.4 with previous version 0.1.2 dated 2015-02-24

Title: Diff, Patch and Merge for Data.frames
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff. The V8 package is used to wrap the 'daff.js' JavaScript library which is included in the package.
Author: Paul Fitzpatrick [aut] (JavaScript original, http://paulfitz.github.io/daff/), Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge

Diff between daff versions 0.1.2 dated 2015-02-24 and 0.1.4 dated 2015-04-18

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 11 files changed, 46 insertions(+), 40 deletions(-)

More information about daff at CRAN
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Package cna updated to version 1.0-3 with previous version 1.0-2 dated 2015-01-03

Title: A Package for Coincidence Analysis (CNA)
Description: Provides functions for performing Coincidence Analysis (CNA).
Author: Ambuehl, Mathias, Michael Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem
Maintainer: Alexis Kauffmann

Diff between cna versions 1.0-2 dated 2015-01-03 and 1.0-3 dated 2015-04-18

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Package cheddar updated to version 0.1-629 with previous version 0.1-626 dated 2014-08-28

Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson

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Package bold updated to version 0.2.6 with previous version 0.2.0 dated 2014-08-20

Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by Bold Systems for genetic barcode data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain

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New package BivarP with initial version 1.0
Package: BivarP
Type: Package
Title: Estimating the Parameters of Some Bivariate Distributions
Version: 1.0
Date: 2015-04-17
Author: Josef Brejcha
Maintainer: Josef Brejcha
Depends: dfoptim, survival, copula
Description: Parameter estimation of bivariate distribution functions modeled as a Archimedean copula function. The input data may contain values from right censored. Used marginal distributions are two-parameter. Methods for density, distribution, survival, random sample generation.
License: GPL (>= 3)
LazyData: TRUE
Packaged: 2015-04-17 10:31:40 UTC; brch
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:55:28

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Fri, 17 Apr 2015

Package VLMC updated to version 1.4-1 with previous version 1.4-0 dated 2014-10-06

Title: Variable Length Markov Chains ('VLMC') Models
Description: Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler
Maintainer: Martin Maechler

Diff between VLMC versions 1.4-0 dated 2014-10-06 and 1.4-1 dated 2015-04-17

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Package TDMR updated to version 1.3 with previous version 1.2 dated 2014-08-30

Title: Tuned Data Mining in R
Description: Tuned Data Mining in R (TDMR) performs a complete tuning of a data mining task.
Author: Wolfgang Konen , Patrick Koch
Maintainer: Wolfgang Konen

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New package marl with initial version 1.0
Package: marl
Type: Package
Title: Multivariate Analysis Based on Relative Likelihoods
Version: 1.0
Date: 2015-04-09
Author: Milan Bimali
Maintainer: Milan Bimali
Description: Functions provided allow data simulation; construction of weighted relative likelihood functions; clustering and principal component analysis based on weighted relative likelihood functions.
License: GPL-2
Packaged: 2015-04-16 22:20:48 UTC; Milan Bimali
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-17 10:41:30

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Thu, 16 Apr 2015

New package multimark with initial version 1.1.3
Package: multimark
Type: Package
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks
Version: 1.1.3
Date: 2015-04-15
Depends: R (>= 3.0.0)
Imports: parallel, statmod, Matrix, RMark, coda, methods, Brobdingnag, mvtnorm
Authors@R: c(person("Brett T.", "McClintock", email = "brett.mcclintock@noaa.gov",role = c("aut", "cre")),person("Acho", "Arnold",role = c("ctb","cph"), comment = "C original matrix library, https://github.com/najela/matrix.h"),person("Barry", "Brown",role = "ctb", comment = "Fortran original ranlib library"),person("James", "Lovato",role = "ctb", comment = "Fortran original ranlib library"),person("John", "Burkardt",role = "ctb", comment = "C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib"),person("Cleve", "Moler",role = "ctb", comment = "C original linpack library, http://www.kkant.net/geist/ranlib/"))
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive "marks", such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo.
License: GPL-2
LazyData: yes
ByteCompile: TRUE
Packaged: 2015-04-16 19:16:16 UTC; Brett McClintock
Author: Brett T. McClintock [aut, cre], Acho Arnold [ctb, cph] (C original matrix library, https://github.com/najela/matrix.h), Barry Brown [ctb] (Fortran original ranlib library), James Lovato [ctb] (Fortran original ranlib library), John Burkardt [ctb] (C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib), Cleve Moler [ctb] (C original linpack library, http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-16 23:32:32

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Package LindenmayeR updated to version 0.1.4 with previous version 0.1-0 dated 2014-08-12

Title: Functions to Explore L-Systems (Lindenmayer Systems)
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson

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Package crunch updated to version 1.1.0 with previous version 1.0.2 dated 2015-04-04

Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson

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Package poweRlaw updated to version 0.30.2 with previous version 0.30.1 dated 2015-03-13

Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie

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New package qclust with initial version 1.0
Package: qclust
Type: Package
Title: Robust Estimation of Gaussian Mixture Models
Version: 1.0
Date: 2015-04-15
Author: Yichen Qin, Carey E. Priebe
Maintainer: Yichen Qin
Description: Robust estimation of Gaussian mixture models fitted by modified EM algorithm, robust clustering and classification.
Depends: mclust, mvtnorm
URL: http://homepages.uc.edu/~qinyn/qclust/
License: GPL-2
Packaged: 2015-04-16 16:10:36 UTC; qyc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-16 19:53:55

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Package mi updated to version 1.0 with previous version 0.10-2 dated 2015-04-07

Title: Missing Data Imputation and Model Checking
Description: The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.
Author: Andrew Gelman [ctb], Jennifer Hill [ctb], Yu-Sung Su [aut], Masanao Yajima [ctb], Maria Pittau [ctb], Ben Goodrich [cre, aut], Yajuan Si [ctb], Jon Kropko [aut]
Maintainer: Ben Goodrich

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Package lsmeans updated to version 2.17 with previous version 2.16 dated 2015-03-14

Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth

Diff between lsmeans versions 2.16 dated 2015-03-14 and 2.17 dated 2015-04-16

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More information about lsmeans at CRAN
Permanent link

New package dga with initial version 1.2
Package: dga
Type: Package
Title: Capture-Recapture Estimation using Bayesian Model Averaging
Version: 1.2
Date: 2015-04-16
Author: James Johndrow, Kristian Lum, and Patrick Ball
Maintainer: Kristian Lum
Description: Performs Bayesian model averaging for capture-recapture. This includes code to stratify records, check the strata for suitable overlap to be used for capture-recapture, and some functions to plot the estimated population size.
License: GPL (>= 2)
LazyLoad: yes
Imports: chron
Packaged: 2015-04-16 14:42:17 UTC; kristianlum
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-16 19:53:41

More information about dga at CRAN
Permanent link

Package compendiumdb updated to version 1.0.0 with previous version 0.1.0 dated 2014-08-29

Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of functional genomics data via a MySQL database.
Author: Umesh K. Nandal and Perry D. Moerland
Maintainer: Umesh Nandal

Diff between compendiumdb versions 0.1.0 dated 2014-08-29 and 1.0.0 dated 2015-04-16

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Package softclassval updated to version 1.0-20150416 with previous version 1.0-20130317 dated 2013-04-03

Title: Soft Classification Performance Measures
Description: An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].
Author: C. Beleites
Maintainer: C. Beleites

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Package RAdwords updated to version 0.1.4 with previous version 0.1.3 dated 2015-04-07

Title: Loading Google Adwords Data into R
Description: Aims at loading Google Adwords data into R. Adwords is an online advertising service that enables advertisers to display advertising copy to web users. Therefore the package implements three main features. First, the package provides an authentication process for R with the Google Adwords API via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.
Author: Johannes Burkhardt , Matthias Bannert
Maintainer: Johannes Burkhardt

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Package letsR updated to version 2.1 with previous version 2.0 dated 2015-02-09

Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on species' distributions and environmental variables as well as species' description and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela

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Package iterpc updated to version 0.2.7 with previous version 0.2.6 dated 2014-11-14

Title: Efficient Iterator for Permutations and Combinations
Description: It helps in 1) generating permutations and combinations with or without replacement; 2) with distinct items or non-distinct items (multiset); 3) calculating number of combinations or permutations in various situations. All generated sequences are in lexicographical order (AKA, dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai

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Package etasFLP updated to version 1.2.1 with previous version 1.2.0 dated 2014-12-22

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present, together with some diagnostic tools. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class 'etasclass').
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

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Package BAT updated to version 1.3.0 with previous version 1.2.1 dated 2015-03-05

Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso

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Package vcdExtra updated to version 0.6-8 with previous version 0.6-5 dated 2015-01-02

Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly

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Package smoother updated to version 1.1 with previous version 1.0.0.0 dated 2014-09-16

Title: Functions Relating to the Smoothing of Numerical Data
Description: A collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton

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Package networksis updated to version 2.1-3 with previous version 2.1-2 dated 2013-05-01

Title: Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
Description: Tools to simulate bipartite networks/graphs with the degrees of the nodes fixed and specified. 'networksis' is part of the 'statnet' suite of packages for network analysis.
Author: Ryan Admiraal and Mark S. Handcock
Maintainer: Ryan Admiraal

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Package copCAR updated to version 1.0-1 with previous version 1.0 dated 2014-09-07

Title: Fitting the copCAR Regression Model for Discrete Areal Data
Description: Provides tools for fitting the copCAR regression model for discrete areal data. Three types of estimation are supported: continuous extension, composite marginal likelihood, and distributional transform.
Author: Emily Goren and John Hughes
Maintainer: John Hughes

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Package BiodiversityR updated to version 2.5-2 with previous version 2.5-1 dated 2014-11-23

Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt

Diff between BiodiversityR versions 2.5-1 dated 2014-11-23 and 2.5-2 dated 2015-04-16

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Wed, 15 Apr 2015

Package rmaf updated to version 3.0.1 with previous version 3.0 dated 2015-04-13

Title: Refined Moving Average Filter
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu

Diff between rmaf versions 3.0 dated 2015-04-13 and 3.0.1 dated 2015-04-15

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Package rjags updated to version 3-15 with previous version 3-14 dated 2014-10-27

Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb]
Maintainer: Martyn Plummer

Diff between rjags versions 3-14 dated 2014-10-27 and 3-15 dated 2015-04-15

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New package rdrop2 with initial version 0.6
Package: rdrop2
Title: Programmatic Interface to the Dropbox API
Version: 0.6
Authors@R: person("Karthik", "Ram", , "karthik.ram@gmail.com", c("aut", "cre"))
Description: Provides full programmatic access to the Dropbox file hosting platform (dropbox.com), including support for all standard file operations.
Depends: R (>= 3.1.1)
License: MIT + file LICENSE
LazyData: true
Imports: assertthat, data.table, dplyr, httr, jsonlite, magrittr
Suggests: testthat, uuid
Packaged: 2015-04-15 15:27:51 UTC; karthik
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:09

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Package rainbow updated to version 3.3 with previous version 3.2 dated 2013-08-28

Title: Rainbow Plots, Bagplots and Boxplots for Functional Data
Description: Functions and data sets for functional data display and outlier detection.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang

Diff between rainbow versions 3.2 dated 2013-08-28 and 3.3 dated 2015-04-15

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New package multiway with initial version 1.0-0
Package: multiway
Type: Package
Title: Component Models for Multi-Way Data
Version: 1.0-0
Date: 2015-04-15
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
Depends: parallel
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints (orthogonality and non-negativity). Fit models include Individual Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
License: GPL (>= 2)
Packaged: 2015-04-15 05:13:48 UTC; Nate
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:04

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Package lctools updated to version 0.2-2 with previous version 0.2 dated 2015-04-05

Title: Local Correlation, Spatial Inequalities and Other Tools
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou

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Package knockoff updated to version 0.2.1 with previous version 0.2 dated 2015-02-05

Title: Knockoff Filter for Controlling the False Discovery Rate
Description: The knockoff filter is a procedure for controlling the false discovery rate (FDR) when performing variable selection. For more information, see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson

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New package forecTheta with initial version 1.0
Package: forecTheta
Type: Package
Title: Forecasting Time Series by Theta Method
Version: 1.0
Date: 2015-03-30
Author: Jose Augusto Fioruci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fioruci
Depends: R (>= 3.0.2), forecast, parallel
Description: Routines for forecasting univariate time series using Theta Method and Optimised Theta Method (Fioruci et al, 2015). Contains two cross-validation routines of Tashman (2000).
License: GPL (>= 2)
URL: http://arxiv.org/abs/1503.03529
Packaged: 2015-04-15 14:02:41 UTC; Augusto
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:01

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