Tue, 26 May 2015

Package RNeXML updated to version 2.0.3 with previous version 2.0.2 dated 2015-05-01

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between RNeXML versions 2.0.2 dated 2015-05-01 and 2.0.3 dated 2015-05-26

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Package Rhpc updated to version 0.15-146 with previous version 0.15-145 dated 2015-05-25

Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R. and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>

Diff between Rhpc versions 0.15-145 dated 2015-05-25 and 0.15-146 dated 2015-05-26

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Package pryr updated to version 0.1.1 with previous version 0.1 dated 2014-07-25

Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the language at a deeper level.
Author: Hadley Wickham [aut, cre], R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between pryr versions 0.1 dated 2014-07-25 and 0.1.1 dated 2015-05-26

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New package MSGLasso with initial version 1.1
Package: MSGLasso
Type: Package
Title: Multivariate Sparse Group Lasso for the Multivariate Multiple Linear Regression with an Arbitrary Group Structure
Version: 1.1
Date: 2015-05-21
Author: Yanming Li <liyanmin@umich.edu>, Bin Nan <bnan@umich.edu>, Ji Zhu <jizhu@umich.edu>
Maintainer: Yanming Li <liyanmin@umich.edu>
Description: For fitting multivariate response and multiple predictor linear regressions with an arbitrary group structure assigned on the regression coefficient matrix, using the multivariate sparse group lasso and the mixed coordinate descent algorithm.
License: GPL (>= 2)
Packaged: 2015-05-21 17:16:28 UTC; User
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-27 01:42:06

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Package laGP updated to version 1.1-5 with previous version 1.1-3 dated 2014-10-31

Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>

Diff between laGP versions 1.1-3 dated 2014-10-31 and 1.1-5 dated 2015-05-26

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Package infuser updated to version 0.2 with previous version 0.1 dated 2015-05-17

Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>

Diff between infuser versions 0.1 dated 2015-05-17 and 0.2 dated 2015-05-26

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Package brms updated to version 0.2.0 with previous version 0.1.0 dated 2015-05-08

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear and ordinal mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>

Diff between brms versions 0.1.0 dated 2015-05-08 and 0.2.0 dated 2015-05-26

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Package aRxiv updated to version 0.5.10 with previous version 0.5.8 dated 2014-12-28

Title: Interface to the arXiv API
Description: An interface to the API for arXiv, a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics.
Author: Karthik Ram [aut], Karl Broman [aut, cre]
Maintainer: Karl Broman <kbroman@biostat.wisc.edu>

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Package synbreed updated to version 0.11-2 with previous version 0.10-5 dated 2014-11-25

Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>

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Package formula.tools updated to version 1.5.2 with previous version 1.3.4 dated 2014-03-20

Title: Utilities for Formulas, Expressions, Calls and Other Objects
Description: These utilities facilitate the programmatic manipulations of formulas, expressions,calls, names, symbols and other objects.
Author: Christopher Brown
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>

Diff between formula.tools versions 1.3.4 dated 2014-03-20 and 1.5.2 dated 2015-05-26

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Package vegan updated to version 2.3-0 with previous version 2.2-1 dated 2015-01-12

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>

Diff between vegan versions 2.2-1 dated 2015-01-12 and 2.3-0 dated 2015-05-26

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More information about vegan at CRAN
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Package lfe updated to version 2.3-1709 with previous version 2.2-1699 dated 2015-04-13

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>

Diff between lfe versions 2.2-1699 dated 2015-04-13 and 2.3-1709 dated 2015-05-26

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Permanent link

Package rpf updated to version 0.45 with previous version 0.44 dated 2014-12-11

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb], Michael D. Hunter [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>

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More information about rpf at CRAN
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Package operator.tools updated to version 1.4.4 with previous version 1.3.0 dated 2012-11-30

Title: Utilities for Working with R's Operators
Description: These utilities allow for programatically working with R's operators: translating between an operator and its underlying function, inverting an operator, determining an operator's type, etc.
Author: Decision Patterns
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>

Diff between operator.tools versions 1.3.0 dated 2012-11-30 and 1.4.4 dated 2015-05-26

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More information about operator.tools at CRAN
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Package soiltexture updated to version 1.3.3 with previous version 1.2.19 dated 2014-09-29

Title: Functions for Soil Texture Plot, Classification and Transformation
Description: "The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
Author: Julien Moeys [aut, cre], Wei Shangguan [ctb], Rainer Petzold [ctb], Budiman Minasny [ctb], Bogdan Rosca [ctb], Nic Jelinski [ctb], Wiktor Zelazny [ctb], Rodolfo Marcondes Silva Souza [ctb], Jose Lucas Safanelli [ctb], Alexandre ten Caten [ctb]
Maintainer: Julien Moeys <jules_m78-soiltexture@yahoo.fr>

Diff between soiltexture versions 1.2.19 dated 2014-09-29 and 1.3.3 dated 2015-05-26

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More information about soiltexture at CRAN
Permanent link

Package Gotoh (with last version 0.9) was removed from CRAN

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

2015-05-22 0.9

Permanent link
Package Rtsne updated to version 0.10 with previous version 0.9 dated 2014-09-18

Title: T-Distributed Stochastic Neighbor Embedding using Barnes-Hut Implementation
Description: An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten.
Author: Jesse Krijthe <jkrijthe@gmail.com>
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>

Diff between Rtsne versions 0.9 dated 2014-09-18 and 0.10 dated 2015-05-26

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New package provenance with initial version 0.1
Package: provenance
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Version: 0.1
Authors@R: person("Pieter", "Vermeesch", , "p.vermeesch@ucl.ac.uk", role = c("aut", "cre"))
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances.
Depends: R (>= 3.0.2)
Imports: MASS, smacof, vegan, shapes
License: GPL-2
LazyData: true
Packaged: 2015-05-26 06:39:29 UTC; pvermees
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-26 09:38:05

More information about provenance at CRAN
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Package drat updated to version 0.0.4 with previous version 0.0.3 dated 2015-04-10

Title: Drat R Archive Template
Description: Creation and Use of R Repositories via two helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between drat versions 0.0.3 dated 2015-04-10 and 0.0.4 dated 2015-05-26

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New package CMplot with initial version 1.0.1
Package: CMplot
Type: Package
Title: Circle Manhattan Plot
Version: 1.0.1
Date: 2015-05-21
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Description: To visualize the results of Genome-Wide Association Study, Manhattan plot was born. However, it will take much time to draw an elaborate one. Here, this package gives a function named "CMplot" can easily solve the problem. Inputting the results of GWAS and adjusting certain parameters, users will obtain the desired Manhattan plot. Also, a circle Manhattan plot is first put forward, which demonstrates multiple traits in one circle plot. A more visualized figure can spare the length of a paper and lift the paper to a higher level.
License: GPL (>= 2)
Depends: R(>= 2.10.0)
Packaged: 2015-05-26 01:46:36 UTC; acer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-26 09:38:02

More information about CMplot at CRAN
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Package shinyjs updated to version 0.0.6.0 with previous version 0.0.3.3 dated 2015-04-22

Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Examples include hiding an element, disabling an input, resetting an input back to its original value, and many more useful functions. Even if you do know JavaScript, shinyjs can be used as convenience functions to avoid dealing with message passing and writing JavaScript code. shinyjs can also be used to easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between shinyjs versions 0.0.3.3 dated 2015-04-22 and 0.0.6.0 dated 2015-05-26

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More information about shinyjs at CRAN
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Package reval updated to version 2.0.0 with previous version 1.0 dated 2015-03-26

Title: Repeated Function Evaluation for Sensitivity Analysis
Description: Simplified scenario testing and sensitivity analysis with R via a generalized function for one-factor-at-a-time (OFAT) sensitivity analysis, evaluation of parameter sets and (sampled) parameter permutations. Options for formatting output and parallel processing are also provided.
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>

Diff between reval versions 1.0 dated 2015-03-26 and 2.0.0 dated 2015-05-26

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New package Rtts with initial version 0.2.5
Package: Rtts
Type: Package
Title: Convert Text into Speech
Depends: RCurl
Version: 0.2.5
Date: 2015-05-26
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Description: Convert text into speech (voice file in .mp3 format) with API offered by Google Translate. Only English is supported currently.
URL: http://r-text-2-speech.r-forge.r-project.org/
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-05-25 23:05:25 UTC; deng
Repository: CRAN
Date/Publication: 2015-05-26 08:03:04

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New package ordinalCont with initial version 0.4
Package: ordinalCont
Title: Ordinal Regression Analysis for Continuous Scales
Version: 0.4
Authors@R: c(person("Maurizio Manuguerra", role = c("aut", "cre"), email = "maurizio.manuguerra@mq.edu.au"), person("Gillian Heller", role = "aut", email = "gillian.heller@mq.edu.au"))
Author: Maurizio Manuguerra [aut, cre], Gillian Heller [aut]
Maintainer: Maurizio Manuguerra <maurizio.manuguerra@mq.edu.au>
Description: A regression framework for response variables which are continuous self-rating scales such as the Visual Analog Scale (VAS) used in pain assessment, or the Linear Analog Self-Assessment (LASA) scales in quality of life studies. These scales measure subjects' perception of an intangible quantity, and cannot be handled as ratio variables because of their inherent nonlinearity. We treat them as ordinal variables, measured on a continuous scale. A function (the g function, currently the generalized logistic function) connects the scale with an underlying continuous latent variable. The link function is the inverse of the CDF of the assumed underlying distribution of the latent variable. Currently the logit link, which corresponds to a standard logistic distribution, is implemented.
Depends: R (>= 3.1.1), fastGHQuad, boot, ucminf
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2015-05-26 05:46:53 UTC; manuguerra
Repository: CRAN
Date/Publication: 2015-05-26 08:24:22

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Package NMF updated to version 0.20.6 with previous version 0.20.5 dated 2014-03-18

Title: Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Description: Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>

Diff between NMF versions 0.20.5 dated 2014-03-18 and 0.20.6 dated 2015-05-26

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Package MixGHD updated to version 1.6 with previous version 1.5 dated 2015-04-30

Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora <ctortora@math.mcmaster.ca>

Diff between MixGHD versions 1.5 dated 2015-04-30 and 1.6 dated 2015-05-26

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Package kernelFactory updated to version 0.2.2 with previous version 0.2.1 dated 2015-05-22

Title: Kernel Factory: An Ensemble of Kernel Machines
Description: Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
Author: Michel Ballings, Dirk Van den Poel
Maintainer: Michel Ballings <Michel.Ballings@GMail.com>

Diff between kernelFactory versions 0.2.1 dated 2015-05-22 and 0.2.2 dated 2015-05-26

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Package crunch updated to version 1.2.1 with previous version 1.1.1 dated 2015-04-20

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 <neal@crunch.io>

Diff between crunch versions 1.1.1 dated 2015-04-20 and 1.2.1 dated 2015-05-26

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 crunch-1.1.1/crunch/vignettes/economist.RData                                                                |only
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 crunch-1.2.1/crunch/.Rinstignore                                                                             |only
 crunch-1.2.1/crunch/DESCRIPTION                                                                              |   10 
 crunch-1.2.1/crunch/MD5                                                                                      |  282 ++---
 crunch-1.2.1/crunch/NAMESPACE                                                                                |    6 
 crunch-1.2.1/crunch/R/AllClasses.R                                                                           |   27 
 crunch-1.2.1/crunch/R/AllGenerics.R                                                                          |    7 
 crunch-1.2.1/crunch/R/append-dataset.R                                                                       |   28 
 crunch-1.2.1/crunch/R/crest.R                                                                                |    2 
 crunch-1.2.1/crunch/R/crunch.R                                                                               |    2 
 crunch-1.2.1/crunch/R/cube-result.R                                                                          |    7 
 crunch-1.2.1/crunch/R/dataset.R                                                                              |    4 
 crunch-1.2.1/crunch/R/new-dataset.R                                                                          |   17 
 crunch-1.2.1/crunch/R/ordering.R                                                                             |    2 
 crunch-1.2.1/crunch/R/share.R                                                                                |   75 +
 crunch-1.2.1/crunch/R/tuple.R                                                                                |    2 
 crunch-1.2.1/crunch/R/variable-order-slots.R                                                                 |   51 -
 crunch-1.2.1/crunch/R/variable-order.R                                                                       |  175 +++
 crunch-1.2.1/crunch/build/vignette.rds                                                                       |binary
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 crunch-1.2.1/crunch/inst/doc/array-variables.html                                                            |   26 
 crunch-1.2.1/crunch/inst/doc/datasets.R                                                                      |   21 
 crunch-1.2.1/crunch/inst/doc/datasets.Rmd                                                                    |    5 
 crunch-1.2.1/crunch/inst/doc/datasets.html                                                                   |    7 
 crunch-1.2.1/crunch/inst/doc/derive.R                                                                        |only
 crunch-1.2.1/crunch/inst/doc/derive.Rmd                                                                      |   71 +
 crunch-1.2.1/crunch/inst/doc/derive.html                                                                     |  106 ++
 crunch-1.2.1/crunch/inst/doc/getting-started.R                                                               |    4 
 crunch-1.2.1/crunch/inst/doc/variable-order.R                                                                |   52 -
 crunch-1.2.1/crunch/inst/doc/variable-order.Rmd                                                              |   78 +
 crunch-1.2.1/crunch/inst/doc/variable-order.html                                                             |  429 ++++++++
 crunch-1.2.1/crunch/inst/doc/variables.R                                                                     |   45 
 crunch-1.2.1/crunch/inst/doc/variables.Rmd                                                                   |    7 
 crunch-1.2.1/crunch/inst/doc/variables.html                                                                  |    8 
 crunch-1.2.1/crunch/man/Categories.Rd                                                                        |    2 
 crunch-1.2.1/crunch/man/CrunchDataset.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/CrunchVariable.Rd                                                                    |    2 
 crunch-1.2.1/crunch/man/ShojiObject-class.Rd                                                                 |    2 
 crunch-1.2.1/crunch/man/Subvariables.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/VariableCatalog.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/VariableOrder-extract.Rd                                                             |   34 
 crunch-1.2.1/crunch/man/VariableOrder-length.Rd                                                              |    2 
 crunch-1.2.1/crunch/man/VariableOrder-slots.Rd                                                               |   32 
 crunch-1.2.1/crunch/man/VariableOrder.Rd                                                                     |    8 
 crunch-1.2.1/crunch/man/appendDataset.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/catalog-extract.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/catalog-length.Rd                                                                    |    2 
 crunch-1.2.1/crunch/man/category-extract.Rd                                                                  |    2 
 crunch-1.2.1/crunch/man/cloneDataset.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/createDataset.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/createWithMetadataAndFile.Rd                                                         |    2 
 crunch-1.2.1/crunch/man/crtabs.Rd                                                                            |    2 
 crunch-1.2.1/crunch/man/crunch-is.Rd                                                                         |    2 
 crunch-1.2.1/crunch/man/crunch-summary.Rd                                                                    |    2 
 crunch-1.2.1/crunch/man/crunch-uni.Rd                                                                        |    2 
 crunch-1.2.1/crunch/man/crunch.Rd                                                                            |    2 
 crunch-1.2.1/crunch/man/crunchAPI.Rd                                                                         |    2 
 crunch-1.2.1/crunch/man/cube-computing.Rd                                                                    |    7 
 crunch-1.2.1/crunch/man/cube-methods.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/dataset-extract.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/dataset-to-R.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/dataset-update.Rd                                                                    |    2 
 crunch-1.2.1/crunch/man/dataset-variables.Rd                                                                 |    2 
 crunch-1.2.1/crunch/man/delete.Rd                                                                            |    2 
 crunch-1.2.1/crunch/man/deleteDataset.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/describe-catalog.Rd                                                                  |    2 
 crunch-1.2.1/crunch/man/describe-category.Rd                                                                 |    2 
 crunch-1.2.1/crunch/man/describe.Rd                                                                          |    2 
 crunch-1.2.1/crunch/man/dichotomize.Rd                                                                       |    2 
 crunch-1.2.1/crunch/man/dim-dataset.Rd                                                                       |    2 
 crunch-1.2.1/crunch/man/expressions.Rd                                                                       |    2 
 crunch-1.2.1/crunch/man/findVariables.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/graftDataset.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/grouped.Rd                                                                           |    2 
 crunch-1.2.1/crunch/man/hiddenVariables.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/hide.Rd                                                                              |    2 
 crunch-1.2.1/crunch/man/hideVariables.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/http-methods.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/index.Rd                                                                             |    2 
 crunch-1.2.1/crunch/man/is-na-categories.Rd                                                                  |    2 
 crunch-1.2.1/crunch/man/listDatasets.Rd                                                                      |    2 
 crunch-1.2.1/crunch/man/loadDataset.Rd                                                                       |    2 
 crunch-1.2.1/crunch/man/login.Rd                                                                             |    2 
 crunch-1.2.1/crunch/man/logout.Rd                                                                            |    2 
 crunch-1.2.1/crunch/man/makeArray.Rd                                                                         |    2 
 crunch-1.2.1/crunch/man/na-omit-categories.Rd                                                                |    2 
 crunch-1.2.1/crunch/man/newDataset.Rd                                                                        |    5 
 crunch-1.2.1/crunch/man/newDatasetByCSV.Rd                                                                   |    5 
 crunch-1.2.1/crunch/man/newDatasetByColumn.Rd                                                                |    6 
 crunch-1.2.1/crunch/man/newDatasetFromFile.Rd                                                                |    2 
 crunch-1.2.1/crunch/man/ordering.Rd                                                                          |    2 
 crunch-1.2.1/crunch/man/prepareBindInputs.Rd                                                                 |    2 
 crunch-1.2.1/crunch/man/refresh.Rd                                                                           |    2 
 crunch-1.2.1/crunch/man/self.Rd                                                                              |    2 
 crunch-1.2.1/crunch/man/session_store.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/share.Rd                                                                             |only
 crunch-1.2.1/crunch/man/shojifyMetadata.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/show-crunch.Rd                                                                       |    2 
 crunch-1.2.1/crunch/man/subvars-extract.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/table.Rd                                                                             |    2 
 crunch-1.2.1/crunch/man/toVariable.Rd                                                                        |    2 
 crunch-1.2.1/crunch/man/tojson-crunch.Rd                                                                     |    4 
 crunch-1.2.1/crunch/man/tuple-methods.Rd                                                                     |    8 
 crunch-1.2.1/crunch/man/type.Rd                                                                              |    2 
 crunch-1.2.1/crunch/man/unbind.Rd                                                                            |    2 
 crunch-1.2.1/crunch/man/updateDatasetList.Rd                                                                 |    2 
 crunch-1.2.1/crunch/man/urls.Rd                                                                              |    2 
 crunch-1.2.1/crunch/man/var-categories.Rd                                                                    |    2 
 crunch-1.2.1/crunch/man/variable-extract.Rd                                                                  |    2 
 crunch-1.2.1/crunch/man/variable-to-R.Rd                                                                     |    2 
 crunch-1.2.1/crunch/man/variable-update.Rd                                                                   |    2 
 crunch-1.2.1/crunch/man/weight.Rd                                                                            |    2 
 crunch-1.2.1/crunch/tests/testthat/api/datasets/dataset1.json                                                |    3 
 crunch-1.2.1/crunch/tests/testthat/api/datasets/dataset1/permissions.json                                    |only
 crunch-1.2.1/crunch/tests/testthat/helper.R                                                                  |    9 
 crunch-1.2.1/crunch/tests/testthat/test-add-variable.R                                                       |    5 
 crunch-1.2.1/crunch/tests/testthat/test-appending.R                                                          |   76 -
 crunch-1.2.1/crunch/tests/testthat/test-cube-errors.R                                                        |    6 
 crunch-1.2.1/crunch/tests/testthat/test-cubes.R                                                              |   16 
 crunch-1.2.1/crunch/tests/testthat/test-dataset.R                                                            |    5 
 crunch-1.2.1/crunch/tests/testthat/test-expression.R                                                         |    4 
 crunch-1.2.1/crunch/tests/testthat/test-graft.R                                                              |   42 
 crunch-1.2.1/crunch/tests/testthat/test-join.R                                                               |   11 
 crunch-1.2.1/crunch/tests/testthat/test-make-array.R                                                         |   14 
 crunch-1.2.1/crunch/tests/testthat/test-new-dataset.R                                                        |   24 
 crunch-1.2.1/crunch/tests/testthat/test-share.R                                                              |only
 crunch-1.2.1/crunch/tests/testthat/test-timing.R                                                             |   24 
 crunch-1.2.1/crunch/tests/testthat/test-update.R                                                             |   41 
 crunch-1.2.1/crunch/tests/testthat/test-variable-catalog.R                                                   |    7 
 crunch-1.2.1/crunch/tests/testthat/test-variable-order.R                                                     |  203 +++-
 crunch-1.2.1/crunch/vignettes/analyze.RData                                                                  |only
 crunch-1.2.1/crunch/vignettes/analyze.Rmd                                                                    |  227 ++++
 crunch-1.2.1/crunch/vignettes/array-variables.RData                                                          |binary
 crunch-1.2.1/crunch/vignettes/datasets.Rmd                                                                   |    5 
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 crunch-1.2.1/crunch/vignettes/derive.Rmd                                                                     |   71 +
 crunch-1.2.1/crunch/vignettes/getting-started.RData                                                          |binary
 crunch-1.2.1/crunch/vignettes/variable-order.RData                                                           |binary
 crunch-1.2.1/crunch/vignettes/variable-order.Rmd                                                             |   78 +
 crunch-1.2.1/crunch/vignettes/variables.RData                                                                |binary
 crunch-1.2.1/crunch/vignettes/variables.Rmd                                                                  |    7 
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Package boxr updated to version 0.2.6 with previous version 0.2.5 dated 2015-04-15

Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box' (https://www.box.com/). In addition to uploading and downloading files, this package includes functions which mirror base R operations for local files, (e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git' style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <rocks.brendan@gmail.com>

Diff between boxr versions 0.2.5 dated 2015-04-15 and 0.2.6 dated 2015-05-26

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Package aroma.core updated to version 2.13.1 with previous version 2.13.0 dated 2015-01-16

Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between aroma.core versions 2.13.0 dated 2015-01-16 and 2.13.1 dated 2015-05-26

 DESCRIPTION                                                |   41 
 MD5                                                        |   50 
 NAMESPACE                                                  |  842 ++++++-------
 NEWS                                                       |   23 
 R/AromaTabularBinaryFile.R                                 |    7 
 R/AromaTransform.R                                         |   33 
 R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R |    6 
 R/RawMirroredAlleleBFractions.R                            |    5 
 man/AromaMicroarrayDataSet.Rd                              |    2 
 man/AromaTabularBinarySet.Rd                               |    2 
 man/AromaUnitCallSet.Rd                                    |    2 
 man/AromaUnitFracBCnBinarySet.Rd                           |    2 
 man/AromaUnitGenotypeCallSet.Rd                            |    2 
 man/AromaUnitPscnBinarySet.Rd                              |    2 
 man/AromaUnitSignalBinarySet.Rd                            |    2 
 man/AromaUnitTotalCnBinarySet.Rd                           |    2 
 man/CbsModel.Rd                                            |   62 
 man/HaarSegModel.Rd                                        |   54 
 man/PairedPSCNData.Rd                                      |    2 
 man/ParametersInterface.Rd                                 |    4 
 man/RawGenomicSignals.Rd                                   |   10 
 man/RawMirroredAlleleBFractions.Rd                         |   26 
 man/UnitNamesFile.Rd                                       |    2 
 man/aroma.core-package.Rd                                  |    2 
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 tests/SegmentedCopyNumbers.R                               |   74 -
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More information about aroma.core at CRAN
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