Tue, 04 Aug 2015

Package MetaLandSim updated to version 0.4 with previous version 0.3 dated 2015-06-24

Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

Diff between MetaLandSim versions 0.3 dated 2015-06-24 and 0.4 dated 2015-08-04

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 15 files changed, 234 insertions(+), 296 deletions(-)

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Package SemiMarkov updated to version 1.4.2 with previous version 1.4.1 dated 2015-04-10

Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <agnieszka.krol@isped.u-bordeaux2.fr>

Diff between SemiMarkov versions 1.4.1 dated 2015-04-10 and 1.4.2 dated 2015-08-04

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Package Rgbp updated to version 1.1.0 with previous version 1.0.9 dated 2015-07-27

Title: Hierarchical Modeling and Frequency Method Checking on Overdispersed Gaussian, Poisson, and Binomial Data
Description: We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>

Diff between Rgbp versions 1.0.9 dated 2015-07-27 and 1.1.0 dated 2015-08-04

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Package rDEA updated to version 1.2-2 with previous version 1.2-1 dated 2015-06-20

Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre], Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>

Diff between rDEA versions 1.2-1 dated 2015-06-20 and 1.2-2 dated 2015-08-04

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Package RcmdrMisc updated to version 1.0-3 with previous version 1.0-2 dated 2014-09-04

Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre], Robert Muenchen [ctb], Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

Diff between RcmdrMisc versions 1.0-2 dated 2014-09-04 and 1.0-3 dated 2015-08-04

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Package InformationValue updated to version 1.1.0 with previous version 1.0.1 dated 2015-07-31

Title: Performance Analysis and Companion Functions for Accuracy Improvement for Binary Classification Problems
Description: Provides companion function for analysing the performance of classification models. Also, provides function to optimise probability cut-off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, etc to aid accuracy improvement in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>

Diff between InformationValue versions 1.0.1 dated 2015-07-31 and 1.1.0 dated 2015-08-04

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Package hamlet updated to version 0.9.4 with previous version 0.7 dated 2014-05-29

Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>

Diff between hamlet versions 0.7 dated 2014-05-29 and 0.9.4 dated 2015-08-04

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Package GoFKernel updated to version 2.0-6 with previous version 2.0-5 dated 2014-12-03

Title: Testing Goodness-of-Fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on a kernel smoothing of the data.
Author: Jose M. Pavia
Maintainer: Jose M. Pavia <Jose.M.Pavia@uv.es>

Diff between GoFKernel versions 2.0-5 dated 2014-12-03 and 2.0-6 dated 2015-08-04

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Package crunch updated to version 1.4.2 with previous version 1.3.2 dated 2015-06-18

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 1.3.2 dated 2015-06-18 and 1.4.2 dated 2015-08-04

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Package BenfordTests updated to version 1.2.0 with previous version 1.1.1 dated 2013-11-04

Title: Statistical Tests for Evaluating Conformity to Benford's Law
Description: Several specialized statistical tests and support functions for determining if numerical data could conform to Benford's law.
Author: Dieter William Joenssen [aut, cre, cph], Thomas Muellerleile [ctb]
Maintainer: Dieter William Joenssen <Dieter.Joenssen@googlemail.com>

Diff between BenfordTests versions 1.1.1 dated 2013-11-04 and 1.2.0 dated 2015-08-04

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Package yakmoR updated to version 0.1.1 with previous version 0.1.0 dated 2015-08-03

Title: A Simple Wrapper for the k-Means Library Yakmo
Description: This is a simple wrapper for the yakmo K-Means library (developed by Naoki Yoshinaga, see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/). It performs fast and robust (orthogonal) K-Means.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>

Diff between yakmoR versions 0.1.0 dated 2015-08-03 and 0.1.1 dated 2015-08-04

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
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Package RcppArmadillo updated to version 0.5.300.4 with previous version 0.5.200.1.0 dated 2015-06-05

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.5.200.1.0 dated 2015-06-05 and 0.5.300.4 dated 2015-08-04

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 inst/include/armadillo_bits/subview_meat.hpp             |   52 +
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More information about RcppArmadillo at CRAN
Permanent link

Mon, 03 Aug 2015

New package xergm.common with initial version 1.5.1
Package: xergm.common
Version: 1.5.1
Date: 2015-08-03
Title: Common Infrastructure for Extensions of Exponential Random Graph Models
Authors@R: person(given = "Philip", family = "Leifeld", email = "philip.leifeld@eawag.ch", role = c("aut", "cre"))
Description: Datasets and definitions of generic functions used in dependencies of the xergm package.
Depends: R (>= 2.14.0), ergm (>= 3.2.4)
Imports: methods, utils
Suggests: xergm
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-08-03 21:47:55 UTC; philip
Author: Philip Leifeld [aut, cre]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Repository: CRAN
Date/Publication: 2015-08-04 00:34:31

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Package RObsDat updated to version 15.08 with previous version 15.02 dated 2015-02-27

Title: Data Management for Hydrology and Beyond Using the Observations Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>

Diff between RObsDat versions 15.02 dated 2015-02-27 and 15.08 dated 2015-08-03

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More information about RObsDat at CRAN
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Package randNames updated to version 0.2.1 with previous version 0.2 dated 2015-04-28

Title: Package Provides Access to Fake User Data
Description: Generates random names with additional information including fake SSNs, gender, location, zip, age, address, and nationality.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between randNames versions 0.2 dated 2015-04-28 and 0.2.1 dated 2015-08-03

 DESCRIPTION       |    6 +++---
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More information about randNames at CRAN
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Package markovchain updated to version 0.4 with previous version 0.3.1 dated 2015-07-07

Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

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More information about markovchain at CRAN
Permanent link

Package httpuv updated to version 1.3.3 with previous version 1.3.2 dated 2014-10-23

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>

Diff between httpuv versions 1.3.2 dated 2014-10-23 and 1.3.3 dated 2015-08-03

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More information about httpuv at CRAN
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Package evolqg updated to version 0.1-6 with previous version 0.1-5 dated 2015-05-22

Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>

Diff between evolqg versions 0.1-5 dated 2015-05-22 and 0.1-6 dated 2015-08-03

 DESCRIPTION                        |   11 +++--
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 R/EvolQG.R                         |    5 ++
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More information about evolqg at CRAN
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Package dr updated to version 3.0.10 with previous version 3.0.9 dated 2014-11-30

Title: Methods for Dimension Reduction for Regression
Description: Functions, methods, and datasets for fitting dimension reduction regression, using slicing (methods SAVE and SIR), Principal Hessian Directions (phd, using residuals and the response), and an iterative IRE. Partial methods, that condition on categorical predictors are also available. A variety of tests, and stepwise deletion of predictors, is also included. Also included is code for computing permutation tests of dimension. Adding additional methods of estimating dimension is straightforward. For documentation, see the vignette in the package. With version 3.0.4, the arguments for dr.step have been modified.
Author: Sanford Weisberg <sandy@umn.edu>,
Maintainer: Sanford Weisberg <sandy@umn.edu>

Diff between dr versions 3.0.9 dated 2014-11-30 and 3.0.10 dated 2015-08-03

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More information about dr at CRAN
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Package taber updated to version 0.1.0 with previous version 0.0.1 dated 2015-07-04

Title: Split and Recombine Your Data
Description: Sometimes you need to split your data and work on the two chunks independently before bringing them back together. 'Taber' allows you to do that with its two functions.
Author: Seth Wenchel [aut, cre, cph]
Maintainer: Seth Wenchel <seth@wenchel.com>

Diff between taber versions 0.0.1 dated 2015-07-04 and 0.1.0 dated 2015-08-03

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Package ReporteRs updated to version 0.8.2 with previous version 0.7.8 dated 2015-03-06

Title: Microsoft Word, Microsoft Powerpoint and HTML Documents Generation
Description: Create Microsoft Word document (>=2007), Microsoft Powerpoint document (>=2007) and HTML documents from R. There are several features to let you format and present R outputs ; e.g. Editable Vector Graphics, functions for complex tables reporting, reuse of corporate template document (*.docx and *.pptx). You can use the package as a tool for fast reporting and as a tool for reporting automation. The package does not require any installation of Microsoft product to be able to write Microsoft files (docx and pptx).
Author: David Gohel [aut, cre], Bootstrap [ctb, cph] (Bootstrap development team), jQuery [ctb, cph] (The jQuery Foundation), Dmitry Baranovskiy [ctb, cph] (raphael javascript libraries)
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>

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Package pedgene updated to version 2.7 with previous version 2.1 dated 2014-06-24

Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut], Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>

Diff between pedgene versions 2.1 dated 2014-06-24 and 2.7 dated 2015-08-03

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More information about pedgene at CRAN
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Package kinship2 updated to version 1.6.4 with previous version 1.6.0 dated 2014-07-22

Title: Pedigree Functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
Author: Terry M Therneau [aut], Schaid Daniel [ctb], Jason Sinnwell [aut, cre], Elizabeth Atkinson [ctb]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>

Diff between kinship2 versions 1.6.0 dated 2014-07-22 and 1.6.4 dated 2015-08-03

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Package D3M updated to version 0.41 with previous version 0.40 dated 2015-08-02

Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>

Diff between D3M versions 0.40 dated 2015-08-02 and 0.41 dated 2015-08-03

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More information about D3M at CRAN
Permanent link

Package aSPU updated to version 1.37 with previous version 1.36 dated 2015-07-28

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.36 dated 2015-07-28 and 1.37 dated 2015-08-03

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New package transcribeR with initial version 0.0.0
Package: transcribeR
Version: 0.0.0
Date: 2015-08-02
Type: Package
Title: Automated Transcription of Audio Files Through the HP IDOL API
Author: Christopher Lucas, Dean Knox, Dustin Tingley, Thomas Scanlan, Shiv Sunil, Michael May, Angela Su
Maintainer: Christopher Lucas <clucas@fas.harvard.edu>
Description: Transcribes audio to text with the HP IDOL API. Includes functions to upload files, retrieve transcriptions, and monitor jobs.
VignetteBuilder: knitr
Imports: httr
Suggests: knitr
License: GPL-3
NeedsCompilation: no
Packaged: 2015-08-03 14:34:21 UTC; christopher
Repository: CRAN
Date/Publication: 2015-08-03 18:53:03

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Package rts updated to version 1.0-10 with previous version 1.0-9 dated 2015-08-02

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-9 dated 2015-08-02 and 1.0-10 dated 2015-08-03

 DESCRIPTION       |   12 ++++++------
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 3 files changed, 10 insertions(+), 10 deletions(-)

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New package pixiedust with initial version 0.1.1
Package: pixiedust
Date: 2015-08-03
Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Version: 0.1.1
Authors@R: person("Benjamin", "Nutter", email = "nutter@battelle.org", role = c("aut", "cre"))
Description: The introduction of the broom package has made converting model objects into data frames as simple as a single function. While the broom package focuses on providing tidy data frames that can be used in advanced analysis, it deliberately stops short of providing functionality for reporting models in publication-ready tables. pixiedust provides this functionality with a programming interface intended to be similar to ggplot2's system of layers with fine tuned control over each cell of the table. Options for output include printing to the console and to the common markdown formats (markdown, HTML, and LaTeX). With a little pixiedust (and happy thoughts) tables can really fly.
Depends: R (>= 3.2.1)
Imports: ArgumentCheck, broom, dplyr, knitr, lazyWeave, magrittr, tidyr
Suggests: testthat
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/nutterb/pixiedust
BugReports: https://github.com/nutterb/pixiedust/issues
NeedsCompilation: no
Packaged: 2015-08-03 11:45:55 UTC; bnutter
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <nutter@battelle.org>
Repository: CRAN
Date/Publication: 2015-08-03 18:52:58

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New package yakmoR with initial version 0.1.0
Package: yakmoR
Type: Package
Title: A Simple Wrapper for the k-Means Library Yakmo
Version: 0.1.0
Date: 2015-07-26
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>
Description: This is a simple wrapper for the yakmo K-Means library (developed by Naoki Yoshinaga, see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/). It performs fast and robust (orthogonal) K-Means.
Copyright: Original GPL-2 C++ code by Naoki Yoshinaga (see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/)
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.6), checkmate (>= 1.5.1), BBmisc (>= 1.9)
LinkingTo: Rcpp
Suggests: knitr, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-08-03 07:35:36 UTC; drunkeneye
Repository: CRAN
Date/Publication: 2015-08-03 11:44:39

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New package repo with initial version 1.0
Package: repo
Type: Package
Title: A Resource Manager for R Objects
Version: 1.0
Date: 2015-07-30
Author: Francesco Napolitano <franapoli@gmail.com>
Maintainer: Francesco Napolitano <franapoli@gmail.com>
Description: This is an R data manager meant to avoid manual storage/retrieval of R data to/from the file system. It builds one (or more) centralized repository where R objects are stored with annotations, tags, dependency notes, provenance traces. It also provides navigation tools to easily locate, load and edit previously stored resources.
License: GPL-3
Imports: digest, tools
Suggests: igraph, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-08-03 09:51:19 UTC; ciccio
Repository: CRAN
Date/Publication: 2015-08-03 12:09:37

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Package maps updated to version 2.3-11 with previous version 2.3-10 dated 2015-07-09

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>. Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between maps versions 2.3-10 dated 2015-07-09 and 2.3-11 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about maps at CRAN
Permanent link

Package mapproj updated to version 1.2-4 with previous version 1.2-3 dated 2015-07-09

Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between mapproj versions 1.2-3 dated 2015-07-09 and 1.2-4 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

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Package mapdata updated to version 2.2-5 with previous version 2.2-4 dated 2015-07-09

Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between mapdata versions 2.2-4 dated 2015-07-09 and 2.2-5 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

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Package cwhmisc updated to version 6.0 with previous version 5.0 dated 2014-10-15

Title: Miscellaneous Functions for Math, Plotting, Printing, Statistics, Strings, and Tools
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
Author: Christian W. Hoffmann <christian@echoffmann.ch> <http://www.echoffmann.ch>
Maintainer: Christian W. Hoffmann <christian@echoffmann.ch>

Diff between cwhmisc versions 5.0 dated 2014-10-15 and 6.0 dated 2015-08-03

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Package ALS updated to version 0.0.6 with previous version 0.0.5 dated 2012-07-02

Title: Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)
Description: Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.
Author: Katharine M. Mullen
Maintainer: Katharine Mullen <mullenkate@gmail.com>

Diff between ALS versions 0.0.5 dated 2012-07-02 and 0.0.6 dated 2015-08-03

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Permanent link

Package ggtern updated to version 1.0.6.0 with previous version 1.0.5.0 dated 2015-04-15

Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>

Diff between ggtern versions 1.0.5.0 dated 2015-04-15 and 1.0.6.0 dated 2015-08-03

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More information about ggtern at CRAN
Permanent link

Package causaleffect updated to version 1.2.0 with previous version 1.1.3 dated 2015-06-30

Title: Deriving Expressions of Joint Interventional Distributions and Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for z-identifiability, transportability, z-transportability and meta-transportability of causal effects by Elias Bareinboim and Judea Pearl. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>

Diff between causaleffect versions 1.1.3 dated 2015-06-30 and 1.2.0 dated 2015-08-03

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Sun, 02 Aug 2015

Package forestFloor updated to version 1.8.3 with previous version 1.5 dated 2015-06-30

Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>

Diff between forestFloor versions 1.5 dated 2015-06-30 and 1.8.3 dated 2015-08-02

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Permanent link

Package D3M updated to version 0.40 with previous version 0.31 dated 2015-07-29

Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>

Diff between D3M versions 0.31 dated 2015-07-29 and 0.40 dated 2015-08-02

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Package brms updated to version 0.4.1 with previous version 0.4.0 dated 2015-07-23

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear 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 0.4.0 dated 2015-07-23 and 0.4.1 dated 2015-08-02

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Package GeneNet updated to version 1.2.13 with previous version 1.2.12 dated 2015-01-20

Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>

Diff between GeneNet versions 1.2.12 dated 2015-01-20 and 1.2.13 dated 2015-08-02

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Package Ecfun updated to version 0.1-6 with previous version 0.1-4 dated 2015-01-27

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>

Diff between Ecfun versions 0.1-4 dated 2015-01-27 and 0.1-6 dated 2015-08-02

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Permanent link

New package trimr with initial version 1.0.0
Package: trimr
Version: 1.0.0
Authors@R: person("James", "Grange", ,"grange.jim@gmail.com", c("aut", "cre"))
Title: An Implementation of Common Response Time Trimming Methods
Description: Provides various commonly-used response time trimming methods, including the recursive / moving-criterion methods reported by Van Selst and Jolicoeur (1994). By passing trimming functions raw data files, the package will return trimmed data ready for inferential testing.
Depends: R (>= 3.1.1)
Imports: stats
License: GPL-3
LazyData: true
URL: www.jimgrange.com
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-08-02 07:43:55 UTC; Home
Author: James Grange [aut, cre]
Maintainer: James Grange <grange.jim@gmail.com>
Repository: CRAN
Date/Publication: 2015-08-02 16:02:46

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Package fast updated to version 0.64 with previous version 0.63 dated 2013-07-08

Title: Implementation of the Fourier Amplitude Sensitivity Test (FAST)
Description: The Fourier Amplitude Sensitivity Test (FAST) is a method to determine global sensitivities of a model on parameter changes with relatively few model runs. This package implements this sensitivity analysis method.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>

Diff between fast versions 0.63 dated 2013-07-08 and 0.64 dated 2015-08-02

 DESCRIPTION     |    8 ++++----
 MD5             |    6 +++---
 NAMESPACE       |    2 ++
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 4 files changed, 11 insertions(+), 9 deletions(-)

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New package dtwclust with initial version 0.1.0
Package: dtwclust
Type: Package
Title: Time Series Clustering with Dynamic Time Warping
Version: 0.1.0
Date: 2015-08-01
Depends: flexclust, proxy, dtw
Imports: stats, methods, caTools, ggplot2, reshape2, modeltools
Suggests: TSdist
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Description: Time series clustering using different techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Additionally, an implementation of k-Shape clustering is available.
URL: https://github.com/asardaes/dtwclust
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-08-02 11:03:32 UTC; Oso
Repository: CRAN
Date/Publication: 2015-08-02 16:02:43

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Package xgboost updated to version 0.4-2 with previous version 0.4-1 dated 2015-08-01

Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.
Author: Tianqi Chen <tianqi.tchen@gmail.com>, Tong He <hetong007@gmail.com>, Michael Benesty <michael@benesty.fr>
Maintainer: Tong He <hetong007@gmail.com>

Diff between xgboost versions 0.4-1 dated 2015-08-01 and 0.4-2 dated 2015-08-02

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Package squash updated to version 1.0.7 with previous version 1.0.6 dated 2014-08-04

Title: Color-Based Plots for Multivariate Visualization
Description: Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, display a matrix as an array of colors, and draw color keys. Higher-level plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.
Author: Aron C. Eklund
Maintainer: Aron C. Eklund <eklund@cbs.dtu.dk>

Diff between squash versions 1.0.6 dated 2014-08-04 and 1.0.7 dated 2015-08-02

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Package rts updated to version 1.0-9 with previous version 1.0-3 dated 2012-11-26

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-3 dated 2012-11-26 and 1.0-9 dated 2015-08-02

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Package mixAK updated to version 4.2 with previous version 4.1-1 dated 2015-07-28

Title: Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between mixAK versions 4.1-1 dated 2015-07-28 and 4.2 dated 2015-08-02

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New package IRISMustangMetrics with initial version 1.0.0
Type: Package
Package: IRISMustangMetrics
Version: 1.0.0
Title: Statistics and Metrics for Seismic Data
Authors@R: c( person("Jonathan", "Callahan", email="jonathan.s.callahan@gmail.com", role=c("aut","cre")), person("Rob", "Casey", email="rob@iris.washington.edu", role=c("aut")), person("Mary", "Templeton", email="met@iris.washington.edu", role=c("aut")) )
Author: Jonathan Callahan [aut, cre], Rob Casey [aut], Mary Templeton [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Depends: R (>= 3.1.0), IRISSeismic (>= 1.0.5)
Imports: methods, pracma, RCurl, seismicRoll (>= 1.0.1), signal, stringr, XML
Collate: Class-Metric.R BSSUtils.R basicStatsMetric.R correlationMetric.R crossCorrelationMetrics.R dailyDCOffsetMetric.R DCOffsetTimesMetric.R gapsMetric.R PSDMetrics.R SNRMetric.R spikesMetric.R STALTAMetric.R stateOfHealthMetric.R upDownTimesMetric.R transferFunctionMetrics.R
Description: Classes and functions for metrics calculation as part of the 'IRIS DMC MUSTANG' project. The functionality in this package builds upon the base classes of the 'IrisSeismic' package. Metrics include basic statistics as well as higher level 'health' metrics that can help identify problematic seismometers.
License: GPL (>= 2)
Repository: CRAN
Packaged: 2015-08-02 01:50:29 UTC; jonathancallahan
NeedsCompilation: no
Date/Publication: 2015-08-02 08:23:09

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Package forecTheta updated to version 1.1 with previous version 1.0 dated 2015-04-15

Title: Forecasting Time Series by Theta Method
Description: Routines for forecasting univariate time series using Theta Method and Optimised Theta Method (Fioruci et al, 2015). Contains several cross-validation routines.
Author: Jose Augusto Fioruci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fioruci <jafioruci@gmail.com>

Diff between forecTheta versions 1.0 dated 2015-04-15 and 1.1 dated 2015-08-02

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Package descr updated to version 1.1.2 with previous version 1.1.1 dated 2015-05-06

Title: Descriptive Statistics
Description: Weighted frequency and contingency tables of categorical variables and of the comparison of the mean value of a numerical variable by the levels of a factor, and methods to produce xtable objects of the tables and to plot them. There are also functions to facilitate the character encoding conversion of objects, to quickly convert fixed width files into csv ones, and to export a data.frame to a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan Kraft
Maintainer: Jakson Aquino <jalvesaq@gmail.com>

Diff between descr versions 1.1.1 dated 2015-05-06 and 1.1.2 dated 2015-08-02

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Sat, 01 Aug 2015

Package partools updated to version 1.1.3 with previous version 1.1.1 dated 2015-07-21

Title: Tools for the 'Parallel' Package
Description: Miscellaneous utilities for the 'parallel' package, cluster-oriented section; "Snowdoop" alternative to MapReduce; file splitting and distributed operations such as sort and aggregate. "Software Alchemy" method for parallelizing most statistical methods, presented in N. Matloff, Parallel Computation for Data Science, Chapman and Hall, 2015. Includes a debugging aid.
Author: Norm Matloff <normmatloff@gmail.com> [aut], Alex Rumbaugh <aprumbaugh@ucdavis.edu> [ctb]
Maintainer: Norm Matloff <normmatloff@gmail.com>

Diff between partools versions 1.1.1 dated 2015-07-21 and 1.1.3 dated 2015-08-01

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Package nplr updated to version 0.1-4 with previous version 0.1-3 dated 2015-07-11

Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. nplr can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre], Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>

Diff between nplr versions 0.1-3 dated 2015-07-11 and 0.1-4 dated 2015-08-01

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Package h5 updated to version 0.9.2 with previous version 0.9.1 dated 2015-05-10

Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The 'HDF5' format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>

Diff between h5 versions 0.9.1 dated 2015-05-10 and 0.9.2 dated 2015-08-01

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New package gendist with initial version 1.0
Package: gendist
Type: Package
Title: Generated Probability Distribution Models
Version: 1.0
Date: 2015-07-30
Author: Shaiful Anuar Abu Bakar
Maintainer: Shaiful Anuar Abu Bakar <saab@um.edu.my>
Description: Computes the probability density function (pdf), cumulative distribution function (cdf), quantile function (qf) and generates random values (rg) for the following general models : mixture models, composite models, folded models, skewed symmetric models and arc tan models.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-08-01 14:29:57 UTC; Soulful
Repository: CRAN
Date/Publication: 2015-08-01 20:34:37

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Package circlize updated to version 0.3.0 with previous version 0.2.5 dated 2015-07-08

Title: Circular Visualization in R
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between circlize versions 0.2.5 dated 2015-07-08 and 0.3.0 dated 2015-08-01

 circlize |only
 1 file changed

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New package xgboost with initial version 0.4-1
Package: xgboost
Type: Package
Title: Extreme Gradient Boosting
Version: 0.4-1
Date: 2015-05-11
Author: Tianqi Chen <tianqi.tchen@gmail.com>, Tong He <hetong007@gmail.com>, Michael Benesty <michael@benesty.fr>
Maintainer: Tong He <hetong007@gmail.com>
Description: Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.
License: Apache License (== 2.0) | file LICENSE
URL: https://github.com/dmlc/xgboost
BugReports: https://github.com/dmlc/xgboost/issues
VignetteBuilder: knitr
Suggests: knitr, ggplot2 (>= 1.0.0), DiagrammeR (>= 0.6), Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3)
Depends: R (>= 2.10)
Imports: Matrix (>= 1.1-0), methods, data.table (>= 1.9.4), magrittr (>= 1.5), stringr (>= 0.6.2)
NeedsCompilation: yes
Packaged: 2015-07-31 23:10:44 UTC; ubuntu
Repository: CRAN
Date/Publication: 2015-08-01 01:24:15

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Package rcbalance updated to version 1.7 with previous version 1.6 dated 2015-05-23

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>

Diff between rcbalance versions 1.6 dated 2015-05-23 and 1.7 dated 2015-08-01

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Package usdm updated to version 1.1-15 with previous version 1.1-12 dated 2013-07-23

Title: Uncertainty Analysis for Species Distribution Models
Description: This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between usdm versions 1.1-12 dated 2013-07-23 and 1.1-15 dated 2015-08-01

 DESCRIPTION |   20 +++---
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Package phonenumber updated to version 0.2.0 with previous version 0.1.0 dated 2015-07-10

Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as on a telephone keypad. When converting letters to numbers, a character vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F" becoming 3, etc. When converting numbers to letters, a character vector is returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and "C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>

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New package Pasha with initial version 0.99.16
Package: Pasha
Type: Package
Title: Preprocessing of Aligned Sequences from HTS Analyses
Version: 0.99.16
Date: 2015-07-01
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil@mssm.edu>
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
License: GPL-3
LazyLoad: yes
Imports: bitops, tools, methods, S4Vectors, IRanges, GenomicRanges, ShortRead, Rsamtools, Biostrings, gtools
Depends: R (>= 3.2.0), parallel, GenomicAlignments
biocViews: ChIPSeq, Sequencing, Software, Preprocessing, Alignment
NeedsCompilation: yes
Packaged: 2015-07-31 20:36:18 UTC; fenouil
Repository: CRAN
Date/Publication: 2015-08-01 07:37:30

More information about Pasha at CRAN
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Package distcomp updated to version 0.25.3 with previous version 0.25.2 dated 2015-07-14

Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre], Marina Bendersky [aut], Sam Gross [aut], Terry M. Therneau [ctb], Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>

Diff between distcomp versions 0.25.2 dated 2015-07-14 and 0.25.3 dated 2015-08-01

 DESCRIPTION  |    6 +++---
 MD5          |    6 +++---
 R/coxstuff.R |    9 ++++++---
 R/distcomp.R |    8 +++++---
 4 files changed, 17 insertions(+), 12 deletions(-)

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Package ConsRank updated to version 0.0.1 with previous version 0.0 dated 2015-07-22

Title: Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>

Diff between ConsRank versions 0.0 dated 2015-07-22 and 0.0.1 dated 2015-08-01

 DESCRIPTION             |    8 ++++----
 MD5                     |    6 +++---
 R/ALL.r                 |   33 ++++++++++++++++++++++++++++++---
 man/ConsRank-package.Rd |    2 --
 4 files changed, 37 insertions(+), 12 deletions(-)

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Permanent link

Fri, 31 Jul 2015

Package ROracle updated to version 1.2-1 with previous version 1.1-12 dated 2014-11-20

Title: OCI Based Oracle Database Interface for R
Description: Oracle database interface (DBI) driver for R. This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Rajendra S. Pingte <rajendra.pingte@oracle.com>

Diff between ROracle versions 1.1-12 dated 2014-11-20 and 1.2-1 dated 2015-07-31

 DESCRIPTION                                     |   12 
 INSTALL                                         |  156 +++++----
 MD5                                             |  176 +++++------
 NAMESPACE                                       |    2 
 NEWS                                            |   26 +
 R/dbi.R                                         |   16 -
 R/oci.R                                         |  245 +++++++++++++--
 configure                                       |   18 -
 configure.ac                                    |    2 
 inst/Copyrights                                 |    2 
 inst/doc/man/de/OraConnection-class.Rd          |    4 
 inst/doc/man/de/Oracle.Rd                       |   50 ++-
 inst/doc/man/de/dbConnect-methods.Rd            |  102 +++---
 inst/doc/man/de/dbDriver-methods.Rd             |   50 +--
 inst/doc/man/de/dbGetInfo-methods.Rd            |  237 ++++++++++++++
 inst/doc/man/de/dbReadTable-methods.Rd          |  374 +++++++++++++++++++----
 inst/doc/man/de/dbSendQuery-methods.Rd          |   65 ++--
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 inst/doc/man/es/OraConnection-class.Rd          |    4 
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 inst/doc/man/es/dbConnect-methods.Rd            |   93 +++--
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 inst/doc/man/ja/dbDriver-methods.Rd             |   47 +-
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 inst/doc/man/ko/OraConnection-class.Rd          |    4 
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 inst/doc/man/ko/dbDriver-methods.Rd             |   38 +-
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 inst/doc/man/ko/dbSendQuery-methods.Rd          |   55 ++-
 inst/doc/man/pt_BR/OraConnection-class.Rd       |    4 
 inst/doc/man/pt_BR/Oracle.Rd                    |   60 ++-
 inst/doc/man/pt_BR/dbConnect-methods.Rd         |  128 ++++----
 inst/doc/man/pt_BR/dbDriver-methods.Rd          |   50 +--
 inst/doc/man/pt_BR/dbGetInfo-methods.Rd         |  241 ++++++++++++++-
 inst/doc/man/pt_BR/dbReadTable-methods.Rd       |  376 +++++++++++++++++++----
 inst/doc/man/pt_BR/dbSendQuery-methods.Rd       |   85 +++--
 inst/doc/man/zh_CN/OraConnection-class.Rd       |    4 
 inst/doc/man/zh_CN/Oracle.Rd                    |   51 ++-
 inst/doc/man/zh_CN/dbConnect-methods.Rd         |  104 +++---
 inst/doc/man/zh_CN/dbDriver-methods.Rd          |   44 +-
 inst/doc/man/zh_CN/dbGetInfo-methods.Rd         |  231 ++++++++++++++
 inst/doc/man/zh_CN/dbReadTable-methods.Rd       |  340 ++++++++++++++++++---
 inst/doc/man/zh_CN/dbSendQuery-methods.Rd       |   57 ++-
 inst/doc/man/zh_TW/OraConnection-class.Rd       |    4 
 inst/doc/man/zh_TW/Oracle.Rd                    |   59 ++-
 inst/doc/man/zh_TW/dbConnect-methods.Rd         |  140 ++++----
 inst/doc/man/zh_TW/dbDriver-methods.Rd          |   46 +-
 inst/doc/man/zh_TW/dbGetInfo-methods.Rd         |  239 ++++++++++++++-
 inst/doc/man/zh_TW/dbListConnections-methods.Rd |    2 
 inst/doc/man/zh_TW/dbReadTable-methods.Rd       |  380 +++++++++++++++++++-----
 inst/doc/man/zh_TW/dbSendQuery-methods.Rd       |   87 +++--
 inst/doc/man/zh_TW/summary-methods.Rd           |    2 
 man/Oracle.Rd                                   |   47 ++
 man/dbDriver-methods.Rd                         |   46 +-
 man/dbGetInfo-methods.Rd                        |   26 +
 man/dbReadTable-methods.Rd                      |  166 +++++++++-
 man/dbSendQuery-methods.Rd                      |   64 ++--
 src/rodbi.c                                     |  285 +++++++++++++++---
 src/rodbi.h                                     |    7 
 src/rooci.c                                     |  159 ++++++----
 src/rooci.h                                     |    6 
 89 files changed, 7679 insertions(+), 2044 deletions(-)

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Package oglmx updated to version 1.0.3 with previous version 1.0.2 dated 2015-06-01

Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>

Diff between oglmx versions 1.0.2 dated 2015-06-01 and 1.0.3 dated 2015-07-31

 DESCRIPTION                 |   10 +-
 MD5                         |   20 ++--
 R/oglmx-functions.R         |  182 +++++++++++++++++++++++++++++++++-----------
 R/oglmx.margins-functions.R |    2 
 build/partial.rdb           |binary
 man/logit.reg.Rd            |   10 +-
 man/oglmx.Rd                |   19 +++-
 man/ologit.reg.Rd           |   10 +-
 man/oprobit.reg.Rd          |   11 ++
 man/probit.reg.Rd           |   10 +-
 man/summary.oglmx.Rd        |    2 
 11 files changed, 202 insertions(+), 74 deletions(-)

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Package multcompView updated to version 0.1-7 with previous version 0.1-5 dated 2012-05-26

Title: Visualizations of Paired Comparisons
Description: Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different. Designed for use in conjunction with the output of functions like TukeyHSD, dist{stats}, simint, simtest, csimint, csimtest{multcomp}, friedmanmc, kruskalmc{pgirmess}.
Author: Spencer Graves, Hans-Peter Piepho and Luciano Selzer with help from Sundar Dorai-Raj
Maintainer: Luciano Selzer <luciano.selzer@gmail.com>

Diff between multcompView versions 0.1-5 dated 2012-05-26 and 0.1-7 dated 2015-07-31

 multcompView-0.1-5/multcompView/NEWS                         |only
 multcompView-0.1-5/multcompView/man/multcompView.package.Rd  |only
 multcompView-0.1-5/multcompView/man/plot.multcomp.Rd         |only
 multcompView-0.1-5/multcompView/man/plotDisplay.Rd           |only
 multcompView-0.1-7/multcompView/DESCRIPTION                  |   30 
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 multcompView-0.1-7/multcompView/NAMESPACE                    |   53 +
 multcompView-0.1-7/multcompView/R/extract_p.R                |   83 +-
 multcompView-0.1-7/multcompView/R/multcompBoxplot.R          |  378 +++++++----
 multcompView-0.1-7/multcompView/R/multcompLetters.R          |  243 +++++++
 multcompView-0.1-7/multcompView/R/multcompTs.R               |  117 +++
 multcompView-0.1-7/multcompView/R/multcompView-package.R     |only
 multcompView-0.1-7/multcompView/R/plot.multcompLetters.R     |  125 +++
 multcompView-0.1-7/multcompView/R/plot.multcompTs.R          |  133 +++
 multcompView-0.1-7/multcompView/R/plotBoxes.R                |   90 ++
 multcompView-0.1-7/multcompView/R/plotLetters.R              |  131 +++
 multcompView-0.1-7/multcompView/R/plotTs.R                   |   91 ++
 multcompView-0.1-7/multcompView/R/print.multcompLetters.R    |   28 
 multcompView-0.1-7/multcompView/R/vec2mat.R                  |   64 +
 multcompView-0.1-7/multcompView/R/vec2mat2.R                 |   36 +
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 multcompView-0.1-7/multcompView/man/multcompLetters.Rd       |  231 ++----
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 33 files changed, 1805 insertions(+), 689 deletions(-)

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Package mcmcse updated to version 1.1-1 with previous version 1.0-1 dated 2012-08-06

Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE computation for expectation and quantile estimators is supported as well as multivariate estimations. The package also provides functions for computing effective sample size and for plotting Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes <hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>

Diff between mcmcse versions 1.0-1 dated 2012-08-06 and 1.1-1 dated 2015-07-31

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 MD5                   |   36 +++++++++++++++++++-----
 NAMESPACE             |   16 ++++++++++
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 23 files changed, 143 insertions(+), 81 deletions(-)

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Package liftr updated to version 0.2 with previous version 0.1 dated 2015-07-15

Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb], Tengfei Yin [ctb], Nan Xiao [aut, cre]
Maintainer: Nan Xiao <nanx@uchicago.edu>

Diff between liftr versions 0.1 dated 2015-07-15 and 0.2 dated 2015-07-31

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 liftr-0.2/liftr/inst/Dockerfile.Rmd       |   11 
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 15 files changed, 218 insertions(+), 307 deletions(-)

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New package iotools with initial version 0.1-12
Package: iotools
Version: 0.1-12
Title: I/O Tools for Streaming
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Taylor Arnold <taylor.arnold@acm.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Depends: R (>= 2.9.0)
Imports: methods, parallel, utils
Suggests: testthat
Description: Basic I/O tools for streaming.
License: GPL-2 | GPL-3
URL: http://www.rforge.net/iotools
NeedsCompilation: yes
Packaged: 2015-07-28 21:46:56 UTC; svnuser
Repository: CRAN
Date/Publication: 2015-07-31 18:02:58

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New package Tmisc with initial version 0.1.1
Package: Tmisc
Title: Turner Miscellaneous
Version: 0.1.1
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Description: Miscellaneous data and utility functions for manipulating data and your R environment.
Depends: R (>= 3.0.0)
Imports: dplyr, utils
License: GPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2015-07-31 13:11:57 UTC; sdt5z
Repository: CRAN
Date/Publication: 2015-07-31 15:32:46

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Package ORCME updated to version 2.0.2 with previous version 2.0.1 dated 2014-07-16

Title: Order Restricted Clustering for Microarray Experiments
Description: Provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>

Diff between ORCME versions 2.0.1 dated 2014-07-16 and 2.0.2 dated 2015-07-31

 DESCRIPTION       |   18 +++++++++---------
 MD5               |    8 ++++----
 NAMESPACE         |    4 +++-
 data/doseData.rda |binary
 data/geneData.rda |binary
 5 files changed, 16 insertions(+), 14 deletions(-)

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Package Kernelheaping updated to version 1.0 with previous version 0.9 dated 2015-06-13

Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>

Diff between Kernelheaping versions 0.9 dated 2015-06-13 and 1.0 dated 2015-07-31

 DESCRIPTION              |    8 +-
 MD5                      |   14 ++--
 NAMESPACE                |   19 +++++
 R/functions.R            |  154 ++++++++++++++++++++++++-----------------------
 data/students.rda        |binary
 man/dbivr.Rd             |    9 +-
 man/dheaping.Rd          |   17 +++--
 man/sim.Kernelheaping.Rd |    2 
 8 files changed, 126 insertions(+), 97 deletions(-)

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Package IsoGene updated to version 1.0-24 with previous version 1.0-23 dated 2014-12-18

Title: Order-Restricted Inference for Microarray Experiments
Description: Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
Author: Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>

Diff between IsoGene versions 1.0-23 dated 2014-12-18 and 1.0-24 dated 2015-07-31

 DESCRIPTION          |   16 ++++++++--------
 MD5                  |   10 +++++-----
 NAMESPACE            |    2 ++
 data/dopamine.rda    |binary
 data/exampleData.rda |binary
 inst/doc/IsoGene.pdf |binary
 6 files changed, 15 insertions(+), 13 deletions(-)

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Package FHtest updated to version 1.3 with previous version 1.2 dated 2015-05-27

Title: Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class
Description: Functions to compare two or more survival curves with: a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes. b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>

Diff between FHtest versions 1.2 dated 2015-05-27 and 1.3 dated 2015-07-31

 FHtest-1.2/FHtest/R/FHtest-internal.R   |only
 FHtest-1.3/FHtest/DESCRIPTION           |    8 ++---
 FHtest-1.3/FHtest/MD5                   |   43 +++++++++++++++-----------------
 FHtest-1.3/FHtest/NAMESPACE             |    4 +-
 FHtest-1.3/FHtest/R/FHtesticp.R         |    2 -
 FHtest-1.3/FHtest/R/FHtesticp.formula.R |   22 ++++++++--------
 FHtest-1.3/FHtest/R/FHtestics.R         |    2 -
 FHtest-1.3/FHtest/R/FHtestics.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/FHtestrcc.R         |    5 +--
 FHtest-1.3/FHtest/R/FHtestrcc.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/FHtestrcp.R         |    5 +--
 FHtest-1.3/FHtest/R/FHtestrcp.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/rcc.R               |   37 ++++++++++++++-------------
 FHtest-1.3/FHtest/R/rcp.R               |   26 ++++++++-----------
 FHtest-1.3/FHtest/man/FHtest-package.Rd |    6 ++--
 FHtest-1.3/FHtest/man/FHtesticp.Rd      |    8 ++---
 FHtest-1.3/FHtest/man/FHtestics.Rd      |    9 ++----
 FHtest-1.3/FHtest/man/FHtestrcc.Rd      |    7 ++---
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 FHtest-1.3/FHtest/man/ics.Rd            |    2 -
 FHtest-1.3/FHtest/man/illust3.Rd        |   37 +++++++++++----------------
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 23 files changed, 155 insertions(+), 171 deletions(-)

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New package EPGLM with initial version 1.0
Package: EPGLM
Type: Package
Title: Gaussian Approximation of Bayesian Binary Regression Models
Version: 1.0
Date: 2015-07-29
Author: James Ridgway
Maintainer: James Ridgway <james.ridgway@ensae.fr>
Description: The main functions compute the expectation propagation approximation of a Bayesian probit/logit models with Gaussian prior. More information can be found in Chopin and Ridgway (2015). More models and priors should follow.
License: GPL (>= 2)
Depends: Rcpp, MASS
LinkingTo: Rcpp, RcppArmadillo, BH
RcppModules: EPprobitCxx, EPlogitCxx
Packaged: 2015-07-31 07:27:52 UTC; james
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-31 13:07:23

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New package ctmm with initial version 0.2.7
Package: ctmm
Version: 0.2.7
Date: 2015-07-27
Title: Continuous-Time Movement Modeling
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Depends: R (>= 2.10)
Imports: expm, graphics, grDevices, manipulate, MASS, Matrix, methods, numDeriv, raster, rgdal, sp, stats, utils
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
License: GPL-3
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-07-28 22:41:12 UTC; Chr
Repository: CRAN
Date/Publication: 2015-07-31 13:08:31

More information about ctmm at CRAN
Permanent link

Package sudokuAlt updated to version 0.1-6 with previous version 0.1-5 dated 2015-07-24

Title: Tools for Making and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods. Solved sudoku games are of some interest in Experimental Design as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>

Diff between sudokuAlt versions 0.1-5 dated 2015-07-24 and 0.1-6 dated 2015-07-31

 DESCRIPTION        |   10 +++++-----
 MD5                |    8 ++++----
 R/sudokuAlt.R      |   21 +++++++++++++--------
 man/fetchAUGame.Rd |   13 ++++++-------
 man/fetchUKGame.Rd |    5 +++++
 5 files changed, 33 insertions(+), 24 deletions(-)

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Package shinyjs updated to version 0.0.8.3 with previous version 0.0.7.0 dated 2015-06-24

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 0.0.7.0 dated 2015-06-24 and 0.0.8.3 dated 2015-07-31

 DESCRIPTION                                           |    6 
 MD5                                                   |   90 ++++-----
 NEWS.md                                               |   24 ++
 R/colourInput.R                                       |   47 +++-
 R/extendShinyjs.R                                     |   20 +-
 R/hidden.R                                            |    2 
 R/inlineCSS.R                                         |    6 
 R/jsFunc-aaa.R                                        |    7 
 R/jsFunc-classFuncs.R                                 |    4 
 R/jsFunc-messageFuncs.R                               |    2 
 R/jsFunc-runjs.R                                      |    2 
 R/jsFunc-stateFuncs.R                                 |    4 
 R/jsFunc-text.R                                       |    2 
 R/jsFunc-visibilityFuncs.R                            |    4 
 R/onclick.R                                           |    6 
 R/reset.R                                             |    6 
 R/useShinyjs.R                                        |    9 
 R/utils.R                                             |   25 --
 README.md                                             |   23 +-
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 inst/examples/basic/app.R                             |    2 
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 inst/examples/demo/server.R                           |    2 
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 man/reset.Rd                                          |    2 
 man/runjs.Rd                                          |    2 
 man/stateFuncs.Rd                                     |    4 
 man/text.Rd                                           |    2 
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 vignettes/overview.Rmd                                |   21 --
 46 files changed, 489 insertions(+), 282 deletions(-)

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Package nlstools updated to version 1.0-2 with previous version 1.0-1 dated 2015-02-26

Title: Tools for Nonlinear Regression Analysis
Description: Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
Author: Florent Baty <florent.baty@gmail.com> and Marie-Laure Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>, with contributions from Sandrine Charles, Jean-Pierre Flandrois, and Christian Ritz
Maintainer: Florent Baty <florent.baty@gmail.com>

Diff between nlstools versions 1.0-1 dated 2015-02-26 and 1.0-2 dated 2015-07-31

 ChangeLog       |    3 +++
 DESCRIPTION     |    8 ++++----
 MD5             |   12 ++++++------
 NAMESPACE       |    4 +++-
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 man/nlstools.Rd |    3 ++-
 7 files changed, 50 insertions(+), 28 deletions(-)

More information about nlstools at CRAN
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Package mipfp updated to version 2.2 with previous version 2.0 dated 2015-03-30

Title: Multidimensional Iterative Proportional Fitting and Alternative Models
Description: An implementation of the iterative proportional fitting (IPFP), maximum likelihood, minimum chi-square and weighted least squares procedures for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional). The package also provides an application of the IPFP to simulate multivariate Bernoulli distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>

Diff between mipfp versions 2.0 dated 2015-03-30 and 2.2 dated 2015-07-31

 DESCRIPTION                 |   13 +
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 NAMESPACE                   |    2 
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 R/ipfp_multi_dim.R          |   24 ++-
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More information about mipfp at CRAN
Permanent link

New package InformationValue with initial version 1.0.1
Package: InformationValue
Type: Package
Title: Performance Analysis and Companion Functions for Binary Classification Problems
Version: 1.0.1
Date: 2015-07-15
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>
Description: Provides companion function for analysing the performance of classification models. Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation for Binary Classification.
License: GPL (>= 2)
LazyData: TRUE
LazyLoad: yes
Depends:
Imports: ggplot2
Packaged: 2015-07-31 04:02:16 UTC; XUZ48472
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-31 09:30:11

More information about InformationValue at CRAN
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Package spsann updated to version 1.0.1 with previous version 1.0.0 dated 2015-07-15

Title: Optimization of Sample Configurations using Spatial Simulated Annealing
Description: Methods to optimize sample configurations using spatial simulated annealing. Multiple objective functions are implemented for various purposes, such as variogram estimation, trend estimation, and spatial interpolation. A general purpose spatial simulated annealing function enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B M Heuvelink [ths], Edzer Pebesma [ctb], Jon Skoien [ctb], Joshua French [ctb], Pierre Roudier [ctb], Dick Brus [ctb], Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

Diff between spsann versions 1.0.0 dated 2015-07-15 and 1.0.1 dated 2015-07-31

 DESCRIPTION                |   50 ++++++++++++++++++++++++---------------------
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More information about spsann at CRAN
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Package quanteda updated to version 0.8.2-0 with previous version 0.8.0-4 dated 2015-07-13

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Pablo Barberá [ctb], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

Diff between quanteda versions 0.8.0-4 dated 2015-07-13 and 0.8.2-0 dated 2015-07-31

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 55 files changed, 3865 insertions(+), 1223 deletions(-)

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Permanent link

New package OTE with initial version 1.0
Package: OTE
Type: Package
Version: 1.0
Title: Optimal Trees Ensembles for Regression, Classification and Class Membership Probability Estimation
Date: 2015-07-31
Author: Zardad Khan, Asma Gul, Aris Perperoglou, Osama Mahmoud, Werner Adler, Miftahuddin and Berthold Lausen
Maintainer: Zardad Khan <zkhan@essex.ac.uk>
Imports: randomForest,stats
Description: Functions for creating ensembles of optimal trees for regression, classification and class membership probability estimation are given. A few trees are selected from an initial set of trees grown by random forest for the ensemble on the basis of their individual and collective performance. Trees are assessed on out-of-bag data and on an independent training data set for individual and collective performance respectively. The prediction functions return estimates of the test responses and their class membership probabilities. Unexplained variations, error rates, confusion matrix, Brier scores, etc. are also returned for the test data.
LazyLoad: yes
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-07-31 03:01:16 UTC; Khan
Repository: CRAN
Date/Publication: 2015-07-31 05:26:54

More information about OTE at CRAN
Permanent link

Thu, 30 Jul 2015

New package rpca with initial version 0.2.3
Package: rpca
Type: Package
Title: RobustPCA: Decompose a Matrix into Low-Rank and Sparse Components
Version: 0.2.3
Date: 2015-07-19
Author: Maciek Sykulski [aut, cre]
Maintainer: Maciek Sykulski <macieksk@gmail.com>
Authors@R: person("Maciek", "Sykulski", email = "macieksk@gmail.com", role = c("aut", "cre"))
Description: Suppose we have a data matrix, which is the superposition of a low-rank component and a sparse component. Candes, E. J., Li, X., Ma, Y., & Wright, J. (2011). Robust principal component analysis?. Journal of the ACM (JACM), 58(3), 11. prove that we can recover each component individually under some suitable assumptions. It is possible to recover both the low-rank and the sparse components exactly by solving a very convenient convex program called Principal Component Pursuit; among all feasible decompositions, simply minimize a weighted combination of the nuclear norm and of the L1 norm. This package implements this decomposition algorithm resulting with Robust PCA approach.
License: GPL-2 | GPL-3
Imports: compiler
NeedsCompilation: no
Packaged: 2015-07-30 22:24:20 UTC; macieksk
Repository: CRAN
Date/Publication: 2015-07-31 01:15:38

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Package rdrop2 updated to version 0.7.0 with previous version 0.6 dated 2015-04-15

Title: Programmatic Interface to the 'Dropbox' API
Description: Provides full programmatic access to the Dropbox file hosting platform (dropbox.com), including support for all standard file operations.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between rdrop2 versions 0.6 dated 2015-04-15 and 0.7.0 dated 2015-07-30

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Package phonTools updated to version 0.2-2.1 with previous version 0.2-2.0 dated 2014-08-04

Title: Tools for Phonetic and Acoustic Analyses
Description: Contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.
Author: Santiago Barreda
Maintainer: Santiago Barreda <sbarreda@ucdavis.edu>

Diff between phonTools versions 0.2-2.0 dated 2014-08-04 and 0.2-2.1 dated 2015-07-30

 DESCRIPTION              |   12 +--
 LICENSE                  |    2 
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 R/vplot.R                |    7 -
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 89 files changed, 468 insertions(+), 354 deletions(-)

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Package optmatch updated to version 0.9-5 with previous version 0.9-3 dated 2014-08-12

Title: Functions for Optimal Matching
Description: Provides routines for distance based bipartite matching to reduce covariate imbalance between treatment and control groups in observational studies. Routines are provided to generate distances from GLM models (propensity score matching) and formulas (Euclidean and Mahalanobis matching), stratified matching (exact matching), and calipers. Results of the fullmatch routine are guaranteed to provide minimum average within matched set distance.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, and Peter Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas <dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>

Diff between optmatch versions 0.9-3 dated 2014-08-12 and 0.9-5 dated 2015-07-30

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 100 files changed, 2392 insertions(+), 2028 deletions(-)

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Package myTAI updated to version 0.3.0 with previous version 0.2.1 dated 2015-07-23

Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological processes to capture evolutionary signals in transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>

Diff between myTAI versions 0.2.1 dated 2015-07-23 and 0.3.0 dated 2015-07-30

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New package MRQoL with initial version 1.0
Package: MRQoL
Type: Package
Title: Minimal Clinically Important Difference and Response Shift Effect for Health-Related Quality of Life
Version: 1.0
Date: 2015-07-30
Author: Ahmad Ousmen
Maintainer: Ahmad Ousmen <ousmen.ahmad@hotmail.com>
Description: We can calculate directly used this package the Minimal Clinically Important Difference by applying the Anchor-based method and the Response shift effect by applying the Then-Test method.
License: GPL (>= 2.0)
NeedsCompilation: no
Packaged: 2015-07-30 16:16:40 UTC; hyper
Repository: CRAN
Date/Publication: 2015-07-31 01:00:10

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Package Harvest.Tree updated to version 1.1 with previous version 1.0 dated 2015-07-10

Title: Harvest the Classification Tree
Description: Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.
Author: Bingyuan Liu/Yan Yuan/Qian Shi
Maintainer: Bingyuan Liu <adler1016@gmail.com>

Diff between Harvest.Tree versions 1.0 dated 2015-07-10 and 1.1 dated 2015-07-30

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Package dendextend updated to version 1.1.0 with previous version 1.0.1 dated 2015-06-28

Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

Diff between dendextend versions 1.0.1 dated 2015-06-28 and 1.1.0 dated 2015-07-30

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Package climwin updated to version 0.1.1 with previous version 0.1.0 dated 2015-07-19

Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@anu.edu.au>

Diff between climwin versions 0.1.0 dated 2015-07-19 and 0.1.1 dated 2015-07-30

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Package plotmo updated to version 3.1.4 with previous version 3.1.3 dated 2015-06-24

Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors while holding the other predictors constant. A poor man's partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

Diff between plotmo versions 3.1.3 dated 2015-06-24 and 3.1.4 dated 2015-07-30

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New package lulcc with initial version 1.0.0
Package: lulcc
Title: Land Use Change Modelling in R
Version: 1.0.0
Author: Simon Moulds <simon.moulds10@imperial.ac.uk>
Maintainer: Simon Moulds <simon.moulds10@imperial.ac.uk>
Description: Classes and methods for spatially explicit land use change modelling in R.
Depends: methods, raster, R (>= 3.1.0)
License: GPL (>= 2)
LazyData: true
Imports: ROCR, lattice, rasterVis
Suggests: caret, rpart, randomForest, gsubfn, Hmisc, plyr, RColorBrewer,
Collate: 'class-CategoryLabel.R' 'class-PredictiveModelList.R' 'class-ObsLulcRasterStack.R' 'class-NeighbRasterStack.R' 'class-ExpVarRasterList.R' 'class-Model.R' 'class-ThreeMapComparison.R' 'AgreementBudget.R' 'ExpVarRasterList.R' 'FigureOfMerit.R' 'Model.R' 'NeighbRasterStack.R' 'ObsLulcRasterStack.R' 'class-PerformanceList.R' 'PerformanceList.R' 'class-PredictionList.R' 'PredictionList.R' 'ThreeMapComparison.R' 'allocate.R' 'allow.R' 'allowNeighb.R' 'approxExtrapDemand.R' 'as.data.frame.R' 'c.PredictiveModelList.R' 'index.R' 'coerce.R' 'compareAUC.R' 'crossTabulate.R' 'data.R' 'getPredictiveModelInputData.R' 'length.R' 'lulcc-package.R' 'models.R' 'names.R' 'partition.R' 'performance.rocr.R' 'plot.AgreementBudget.R' 'plot.FigureOfMerit.R' 'plot.Performance.R' 'plot.R' 'predict.R' 'resample.R' 'show.R' 'subset.R' 'summary.R' 'total.R'
Packaged: 2015-07-30 09:29:23 UTC; simon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-30 13:13:50

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Package cmsaf updated to version 1.5 with previous version 1.4 dated 2015-06-26

Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable observing of the climate system by providing Essential Climate Variables related to the energy and water cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven National Meteorological and Hydrological Services, including the Deutscher Wetterdienst (DWD). The cmsaf R-package provides a small collection of R-functions, which are inspired by the Climate Data Operators (cdo). This gives the opportunity to analyse and manipulate CM SAF data without the need of installing cdo. The cmsaf R-package is tested for CM SAF netcdf data, which are structured in three-dimensional arrays (longitude, latitude, time) on a rectangular grid. Layered CM SAF data have to be converted with the provided `levbox_mergetime` function. The cmsaf R-package functions have only minor checks for deviations from the recommended data structure, and give only few specific error messages. Thus, there is no warranty of accurate results. A Windows binary file and scripts for an easy application of the functions are provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

Diff between cmsaf versions 1.4 dated 2015-06-26 and 1.5 dated 2015-07-30

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Package randtoolbox updated to version 1.17 with previous version 1.16 dated 2014-12-05

Title: Toolbox for Pseudo and Quasi Random Number Generation and RNG Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some RNG tests - the gap test, the serial test, the poker test. The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package. A number of RNGs and tests for RNGs are also provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

Diff between randtoolbox versions 1.16 dated 2014-12-05 and 1.17 dated 2015-07-30

 DESCRIPTION              |   12 ++++++------
 LICENSE                  |    6 +++---
 MD5                      |   27 ++++++++++++++-------------
 NAMESPACE                |    7 +++++--
 R/quasiRNG.R             |   12 ++++--------
 build/vignette.rds       |binary
 configure.ac             |    4 ++--
 inst/NEWS                |   15 +++++++++++++++
 inst/doc/fullpres.R      |    2 +-
 inst/doc/fullpres.pdf    |binary
 inst/doc/shortintro.R    |    2 +-
 inst/doc/shortintro.pdf  |binary
 man/overall-doc.Rd       |   17 ++++++++---------
 man/pseudoRNG.Rd         |    2 +-
 tests/test-sobol-scram.R |only
 15 files changed, 60 insertions(+), 46 deletions(-)

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Package CDVine updated to version 1.3 with previous version 1.2 dated 2014-03-27

Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine) and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate as well as vine copula selection are provided. Models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are also included. Data is assumed to lie in the unit hypercube (so-called copula data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>

Diff between CDVine versions 1.2 dated 2014-03-27 and 1.3 dated 2015-07-30

 DESCRIPTION           |   23 
 MD5                   |   62 +-
 NAMESPACE             |   73 +--
 R/BiCopCDF.r          |  148 +++---
 R/BiCopChiPlot.r      |  255 +++++-----
 R/BiCopEst.R          | 1178 ++++++++++++++++++++++++--------------------------
 R/BiCopGofKendall.r   |  498 ++++++++++-----------
 R/BiCopHfunc.r        |  145 +++---
 R/BiCopIndTest.r      |   36 -
 R/BiCopLambda.r       |  511 ++++++++++-----------
 R/BiCopMetaContour.r  |  848 +++++++++++++++++------------------
 R/BiCopName.r         |  232 ++++-----
 R/BiCopPDF.r          |  109 +++-
 R/BiCopPar2TailDep.r  |  220 ++++-----
 R/BiCopPar2Tau.r      |  305 ++++++------
 R/BiCopSelect.r       |  689 ++++++++++++++---------------
 R/BiCopSim.R          |   10 
 R/BiCopTau2Par.r      |   74 +--
 R/BiCopVuongClarke.r  |  384 +++++++---------
 R/CDVineAIC.R         |  300 +++++++-----
 R/CDVineClarkeTest.r  |  369 +++++++++------
 R/CDVineCopSelect.R   |  272 +++++------
 R/CDVineLogLik.R      |  211 ++++----
 R/CDVineMLE.R         |  690 +++++++++++++++--------------
 R/CDVinePar2Tau.r     |  127 +++--
 R/CDVineSeqEst.R      |  507 ++++++++++-----------
 R/CDVineSim.R         |  487 ++++++++++----------
 R/CDVineTreePlot.R    |  642 +++++++++++++--------------
 R/CDVineVuongTest.r   |  376 +++++++++------
 R/zzz.R               |    5 
 inst/ChangeLog        |    8 
 man/CDVine-package.Rd |   11 
 32 files changed, 5087 insertions(+), 4718 deletions(-)

More information about CDVine at CRAN
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New package bnclassify with initial version 0.3.0
Package: bnclassify
Title: Learning Bayesian Network Classifiers from Data
Description: Implementation of different algorithms for learning discrete Bayesian network classifiers from data, including wrapper algorithms and those based on Chow-Liu's algorithm.
Version: 0.3.0
Authors@R: c(person("Mihaljevic","Bojan",email="bmihaljevic@fi.upm.es",role=c("aut","cre")), person("Bielza","Concha",email="mcbielza@fi.upm.es",role="aut"), person("Larranaga","Pedro",email="pedro.larranaga@fi.upm.es",role="aut"))
URL: http://github.com/bmihaljevic/bnclassify
BugReports: http://github.com/bmihaljevic/bnclassify/issues
Depends: R (>= 3.2.0)
Imports: assertthat (>= 0.1), entropy(>= 1.2.0), crossval(>= 1.0.2), graph(>= 1.42.0), matrixStats(>= 0.14.0), RBGL(>= 1.40.1), rpart(>= 4.1-8)
Suggests: gRain(>= 1.2-3), gRbase(>= 1.7-0.1), mlr(>= 2.2), testthat(>= 0.8.1), knitr(>= 1.10.5), microbenchmark(>= 1.4-2), ParamHelpers(>= 1.5), Rgraphviz(>= 2.8.1), rmarkdown(>= 0.7)
License: GPL (>= 2)
Author: Mihaljevic Bojan [aut, cre], Bielza Concha [aut], Larranaga Pedro [aut]
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-07-30 08:14:36 UTC; Bojan
Repository: CRAN
Date/Publication: 2015-07-30 11:27:47

More information about bnclassify at CRAN
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