Tue, 07 Apr 2015

Package TSPred updated to version 2.0 with previous version 1.0 dated 2015-03-30

Title: Functions for Baseline-Based Time Series Prediction
Description: Functions for time series prediction and accuracy assessment using automatic ARIMA modelling. The generated ARIMA models and its yielded prediction errors are intended to be used as baseline for evaluating the practical value of other time series prediction methods and creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ), Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles

Diff between TSPred versions 1.0 dated 2015-03-30 and 2.0 dated 2015-04-07

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Package TriMatch updated to version 0.9.4 with previous version 0.9.1 dated 2013-09-20

Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer
Maintainer: Jason Bryer

Diff between TriMatch versions 0.9.1 dated 2013-09-20 and 0.9.4 dated 2015-04-07

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Package softImpute updated to version 1.4 with previous version 1.0 dated 2013-04-03

Title: Matrix Completion via Iterative Soft-Thresholded SVD
Description: Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an "EM" flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components)
Author: Trevor Hastie and Rahul Mazumder
Maintainer: Trevor Hastie

Diff between softImpute versions 1.0 dated 2013-04-03 and 1.4 dated 2015-04-07

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Package searchable updated to version 0.3.3.1 with previous version 0.1.2 dated 2015-03-24

Title: Tools for Custom Searches / Subsets / Slices of Named R Objects
Description: Provides functionality for searching / subsetting and slicing named objects using 'stringr/i'-style modifiers by case (in)sensitivity, regular expressions or fixed expressions; searches uses the standard '[' operator and allows specification of default search behavior to either the search target (named object) and/or the search pattern.
Author: "DecisionPatterns [aut, cre]"
Maintainer: Christopher Brown

Diff between searchable versions 0.1.2 dated 2015-03-24 and 0.3.3.1 dated 2015-04-07

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Package PhyloMeasures updated to version 1.1 with previous version 1.0 dated 2015-04-02

Title: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures
Description: Given a phylogenetic tree T and a sample S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers the implementations of efficient algorithms for several such measures. Most importantly, the package includes algorithms for computing exactly and efficiently the expectation and the variance of these measures, which are essential for null model comparisons. Efficient computation of richness-standardized versions of these metrics, such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures are also available in this package. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure.
Author: Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Maintainer: Constantinos Tsirogiannis

Diff between PhyloMeasures versions 1.0 dated 2015-04-02 and 1.1 dated 2015-04-07

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Package phangorn updated to version 1.99-13 with previous version 1.99-12 dated 2015-02-13

Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep

Diff between phangorn versions 1.99-12 dated 2015-02-13 and 1.99-13 dated 2015-04-07

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Package NCmisc updated to version 1.1.4 with previous version 1.1.3 dated 2014-09-03

Title: Miscellaneous Functions for Creating Adaptive Functions and Scripts
Description: A set of handy functions. Includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper

Diff between NCmisc versions 1.1.3 dated 2014-09-03 and 1.1.4 dated 2015-04-07

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Package nanop updated to version 2.0-5 with previous version 2.0-4 dated 2014-08-25

Title: Tools for Nanoparticle Simulation and Calculation of PDF and Total Scattering Structure Function
Description: This software package implements functions to simulate spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal structures and to calculate the associated pair-distribution function and X-ray/neutron total-scattering signals. It also provides a target function that can be used for simultaneous fitting of small- and wide-angle total scattering data in real and reciprocal spaces. The target function can be generated either as a sum of weighted residuals for individual datasets or as a vector of residuals suitable for optimization using multi-criteria algorithms (e.g. Pareto methods).
Author: Anton Gagin, Katharine Mullen, Igor Levin
Maintainer: Anton Gagin

Diff between nanop versions 2.0-4 dated 2014-08-25 and 2.0-5 dated 2015-04-07

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Package NAM updated to version 1.2 with previous version 1.1.2 dated 2015-04-01

Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier

Diff between NAM versions 1.1.2 dated 2015-04-01 and 1.2 dated 2015-04-07

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New package esaBcv with initial version 1.0.1
Package: esaBcv
Title: Estimate Number of Latent Factors and Factor Matrix for Factor Analysis
Version: 1.0.1
Authors@R: c(person(c("Art", "B."), "Owen", role = c("aut")), person("Jingshu", "Wang", email = "wangjingshususan@gmail.com", role = c("aut", "cre")) )
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Depends: R (>= 3.1.3)
License: GPL (>= 2)
LazyData: true
Imports: corpcor, svd
Suggests: MASS
Packaged: 2015-04-07 18:23:26 UTC; jingshu
Author: Art B. Owen [aut], Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 00:53:20

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Package R2OpenBUGS updated to version 3.2-3.1 with previous version 3.2-2.2 dated 2013-04-10

Title: Running OpenBUGS from R
Description: Using this package, it is possible to call a BUGS model, summarize inferences and convergence in a table and graph, and save the simulations in arrays for easy access in R.
Author: originally written as R2WinBUGS by Andrew Gelman ; changes and packaged by Sibylle Sturtz and Uwe Ligges . With considerable contributions by Gregor Gorjanc and Jouni Kerman . Adapted to R2OpenBUGS from R2WinBUGS by Neal Thomas.
Maintainer: Neal Thomas

Diff between R2OpenBUGS versions 3.2-2.2 dated 2013-04-10 and 3.2-3.1 dated 2015-04-07

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Package network updated to version 1.12.0 with previous version 1.11.3 dated 2014-12-06

Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre], David Hunter [ctb], Mark Handcock [ctb], Skye Bender-deMoll [ctb], Jeffrey Horner [ctb]
Maintainer: Carter T. Butts

Diff between network versions 1.11.3 dated 2014-12-06 and 1.12.0 dated 2015-04-07

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Package Deriv updated to version 3.2 with previous version 3.0 dated 2015-03-06

Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.
Author: Andrew Clausen [aut], Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol

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Package BGLR updated to version 1.0.4 with previous version 1.0.3 dated 2014-06-10

Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez

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Package Formula updated to version 1.2-1 with previous version 1.2-0 dated 2015-01-19

Title: Extended Model Formulas
Description: Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.
Author: Achim Zeileis [aut, cre], Yves Croissant [aut]
Maintainer: Achim Zeileis

Diff between Formula versions 1.2-0 dated 2015-01-19 and 1.2-1 dated 2015-04-07

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Package rehh updated to version 1.12 with previous version 1.11 dated 2013-08-26

Title: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests
Description: Functions for the detection of footprints of selection on dense SNP data using Extended Homozygosity Haplotype (EHH) based tests. The package includes computation of EHH, iHS (within population) and Rsb (across pairs of populations) statistics. Various plotting functions are also included to facilitate visualization and interpretation of the results.
Author: Mathieu Gautier and Renaud Vitalis
Maintainer: Mathieu Gautier

Diff between rehh versions 1.11 dated 2013-08-26 and 1.12 dated 2015-04-07

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Package RAdwords updated to version 0.1.3 with previous version 0.1.2 dated 2015-03-27

Title: Loading Google Adwords Data into R
Description: The aim of RAdwords is loading Adwords data into R. Therefore the package implements three main features. First, the package provides an authentication process for R with the 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

Diff between RAdwords versions 0.1.2 dated 2015-03-27 and 0.1.3 dated 2015-04-07

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New package quanteda with initial version 0.7.2
Package: quanteda
Type: Package
Title: Quantitative Analysis of Textual Data
Authors@R: c( person("Kenneth", "Benoit", email = "kbenoit@lse.ac.uk", role = c("aut", "cre")), person("Paul", "Nulty", email = "paul.nulty@gmail.com", role = "aut"), person("Pablo", "Barberá", email = "pablo.barbera@nyu.edu", role = "ctb"), person("Kohei", "Watanabe", email = "watanabe.kohei@gmail.com", role = "ctb"), person("Benjamin", "Lauderdale", email = "B.E.lauderdale@lse.ac.uk", role = "ctb"))
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Pablo Barberá [ctb], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb]
Version: 0.7.2
Date: 2015-04-05
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
License: GPL-3
Depends: R (>= 3.0)
Imports: methods, Matrix (>= 1.1), data.table (>= 1.9.3), SnowballC, wordcloud, proxy, Rcpp, ca
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, lda, topicmodels, jsonlite (>= 0.9.10), streamR, tm, slam, ggplot2
URL: http://github.com/kbenoit/quanteda
Encoding: UTF-8
BugReports: https://github.com/kbenoit/quanteda/issues
LazyData: TRUE
VignetteBuilder: knitr
Collate: 'RcppExports.R' 'clean.R' 'dictionaryFunctions.R' 'collocations.R' 'converters.R' 'corpus-sources-S4.R' 'corpus.R' 'dataDocs.R' 'describe-texts.R' 'dfm-classes.R' 'dfm-main.R' 'distance.R' 'gui.R' 'kwic.R' 'lexdiv.R' 'ngrams.R' 'onLoad.R' 'plots.R' 'quanteda-package.R' 'resample.R' 'settings.R' 'stopwords.R' 'syllables.R' 'textmodel-ca.R' 'textmodel-generics.R' 'textmodel-wordfish.R' 'textmodel-wordscores.R' 'tokenize.R'
Packaged: 2015-04-07 12:03:05 UTC; kbenoit
Maintainer: Kenneth Benoit
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-07 16:00:23

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Package mi updated to version 0.10-2 with previous version 0.10-1 dated 2015-04-06

Title: Missing Data Imputation and Model Checking
Description: R functions for performing multiple imputation with several checks.
Author: Andrew Gelman , Jennifer Hill , Yu-Sung Su , Masanao Yajima , Maria Grazia Pittau
Maintainer: Yu-Sung Su

Diff between mi versions 0.10-1 dated 2015-04-06 and 0.10-2 dated 2015-04-07

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New package HelpersMG with initial version 1.0
Package: HelpersMG
Type: Package
Title: Tools for Earth Meteorological Analysis
Version: 1.0
Date: 2015-04-07
Author: Marc Girondot
Maintainer: Marc Girondot
Depends: coda, R (>= 2.14.0)
Suggests: RNetCDF, ncdf4, ncdf, maps, XML
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct daily time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
License: GPL-2
LazyData: yes
LazyLoad: yes
Encoding: UTF-8
Packaged: 2015-04-07 13:27:22 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-07 15:40:53

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Package dygraphs updated to version 0.4.3 with previous version 0.4.2 dated 2015-03-04

Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the dygraphs JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib, http://dygraphs.com/), JJ Allaire [aut, cre] (R interface), RStudio [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire

Diff between dygraphs versions 0.4.2 dated 2015-03-04 and 0.4.3 dated 2015-04-07

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Package arm updated to version 1.8-4 with previous version 1.8-03 dated 2015-04-03

Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut], Yu-Sung Su [aut, cre], Masanao Yajima [ctb], Jennifer Hill [ctb], Maria Grazia Pittau [ctb], Jouni Kerman [ctb], Tian Zheng [ctb], Vicent Dorie [ctb]
Maintainer: Yu-Sung Su

Diff between arm versions 1.8-03 dated 2015-04-03 and 1.8-4 dated 2015-04-07

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Package userfriendlyscience updated to version 0.2-2 with previous version 0.2-1 dated 2015-03-23

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 0.2-1 dated 2015-03-23 and 0.2-2 dated 2015-04-07

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Package rcorpora updated to version 1.0.1 with previous version 1.0.0 dated 2015-04-07

Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data. It contains all data sets from https://github.com/dariusk/corpora. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson, Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup, Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern, Ross Barclay, Ross Binden, Justin Alford, Cole Willsea, Andrew Gorman, Javier Arce, Patrick Rodriguez, Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody, Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black, Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell, Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi

Diff between rcorpora versions 1.0.0 dated 2015-04-07 and 1.0.1 dated 2015-04-07

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Package StereoMorph updated to version 1.4 with previous version 1.3 dated 2015-02-12

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen

Diff between StereoMorph versions 1.3 dated 2015-02-12 and 1.4 dated 2015-04-07

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Package RDML updated to version 0.8-2 with previous version 0.4-2 dated 2014-09-10

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages.
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh

Diff between RDML versions 0.4-2 dated 2014-09-10 and 0.8-2 dated 2015-04-07

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New package rcorpora with initial version 1.0.0
Package: rcorpora
Title: A Collection of Small Text Corpuses of Interesting Data
Version: 1.0.0
Maintainer: Gabor Csardi
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson, Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup, Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern, Ross Barclay, Ross Binden, Justin Alford, Cole Willsea, Andrew Gorman, Javier Arce, Patrick Rodriguez, Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody, Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black, Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell, Michael Dewberry, Joe Mahoney
Description: A collection of small text corpuses of interesting data. It contains all data sets from the fantastic https://github.com/dariusk/corpora repository. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
License: CC0
Imports: jsonlite
URL: https://github.com/gaborcsardi/rcorpora
BugReports: https://github.com/gaborcsardi/rcorpora/issues
NeedsCompilation: no
Packaged: 2015-04-07 02:22:26 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2015-04-07 09:10:08

More information about rcorpora at CRAN
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