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

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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

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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

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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

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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

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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

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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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