Mon, 27 Jul 2015

Package WiSEBoot updated to version 1.1.0 with previous version 1.0.0 dated 2015-07-06

Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction. Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>

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Package stm updated to version 1.1.0 with previous version 1.0.8 dated 2014-11-07

Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart <bms4@princeton.edu>

Diff between stm versions 1.0.8 dated 2014-11-07 and 1.1.0 dated 2015-07-27

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Package smoothSurv updated to version 1.6 with previous version 1.5-2 dated 2015-05-21

Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

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Package SciencesPo updated to version 1.3.6 with previous version 1.3.5 dated 2015-07-15

Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>

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New package Rgbp with initial version 1.0.9
Package: Rgbp
Version: 1.0.9
Date: 2015-07-27
Title: Hierarchical Modeling and Frequency Method Checking on Overdispersed Gaussian, Poisson, and Binomial Data
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>
Depends: R (>= 2.2.0), sn (>= 0.4-18), mnormt (>= 1.5-1)
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.
License: GPL-2
BugReports: https://github.com/jyklly/Rgbp/issues
Packaged: 2015-07-27 18:17:48 UTC; josephkelly
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-27 23:56:24

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Package RcmdrPlugin.NMBU updated to version 1.8.3 with previous version 1.8.0.4 dated 2015-03-12

Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre], Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between RcmdrPlugin.NMBU versions 1.8.0.4 dated 2015-03-12 and 1.8.3 dated 2015-07-27

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Package phyext2 updated to version 0.0.4 with previous version 0.0.3 dated 2015-07-17

Title: An Extension (for Package 'SigTree') of Some of the Classes in Package 'phylobase'
Description: Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
Author: J. Conrad Stack
Maintainer: John R. Stevens <john.r.stevens@usu.edu>

Diff between phyext2 versions 0.0.3 dated 2015-07-17 and 0.0.4 dated 2015-07-27

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New package QFRM with initial version 1.0.1
Package: QFRM
Type: Package
Title: Pricing of Vanilla and Exotic Option Contracts
Version: 1.0.1
Date: 2015-06-28
Maintainer: Oleg Melnikov <XisReal@gmail.com>
Authors@R: c( person("Oleg", "Melnikov", role = c("aut", "cre"), email = "XisReal@gmail.com"), person("Max", "Lee", role = "ctb", email = "max.lee@rice.edu"), person("Robert", "Abramov", role = "ctb", email = "rha1@rice.edu"), person("Richard", "Huang", role = "ctb", email = "richard.b.huang@rice.edu"), person("Liu", "Tong", role = "ctb", email = "tong.liu@rice.edu"), person("Jake", "Kornblau", role = "ctb", email = "jake.a.kornblau@rice.edu"), person("Xinnan", "Lu", role = "ctb", email = "xinnan.lu@rice.edu"), person("Kiryl", "Novikau", role = "ctb", email = "kiryl.novikau@rice.edu"), person("Tongyue", "Luo", role = "ctb", email = "tongyue.luo@rice.edu"), person("Le", "You", role = "ctb", email = "le.you@rice.edu"), person("Jin", "Chen", role = "ctb", email = "jin.chen@rice.edu"), person("Chengwei", "Ge", role = "ctb", email = "chengwei.ge@rice.edu"), person("Jiayao", "Huang", role = "ctb", email = "jiayao.huang@rice.edu"), person("Kim", "Raath", role = "ctb", email = "kcr2@rice.edu") )
Description: Option pricing (financial derivatives) techniques mainly following textbook 'Options, Futures and Other Derivatives', 9ed by John C.Hull, 2014. Prentice Hall. Implementations are via binomial tree option model (BOPM), Black-Scholes model, Monte Carlo simulations, etc. This package is a result of Quantitative Financial Risk Management course (STAT 449 and STAT 649) at Rice University, Houston, TX, USA, taught by Oleg Melnikov, statistics PhD student, as of Spring 2015.
Repository: CRAN
License: GPL (>= 2)
URL: http://Oleg.Rice.edu
NeedsCompilation: no
Depends: R (>= 2.14.0)
LazyLoad: yes
LazyData: yes
Imports: stats,methods,graphics
Packaged: 2015-07-27 22:28:29 UTC; Oleggio
Author: Oleg Melnikov [aut, cre], Max Lee [ctb], Robert Abramov [ctb], Richard Huang [ctb], Liu Tong [ctb], Jake Kornblau [ctb], Xinnan Lu [ctb], Kiryl Novikau [ctb], Tongyue Luo [ctb], Le You [ctb], Jin Chen [ctb], Chengwei Ge [ctb], Jiayao Huang [ctb], Kim Raath [ctb]
X-CRAN-Comment: Archived on 2015-05-08 as the maintainer <oleg.melnikov@rice.edu> said he is still collecting functions from his students and cleaning up the apparently unfinished package.
Date/Publication: 2015-07-28 00:48:16

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New package params with initial version 0.2
Package: params
Type: Package
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options().
Version: 0.2
Date: 2015-07-10
Depends: whisker
Imports: knitr, utils
Suggests: openxlsx
URL: https://github.com/sahilseth/params
BugReports: https://github.com/sahilseth/params/issues
Authors@R: c(person("Sahil", "Seth", role = c("aut", "cre"), email = "me@sahilseth.com"))
License: GPL-2
NeedsCompilation: no
Packaged: 2015-07-27 16:54:21 UTC; sahilseth
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Repository: CRAN
Date/Publication: 2015-07-28 00:11:50

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Package MPTinR updated to version 1.10.3 with previous version 1.9.2 dated 2015-06-13

Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>

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Package FastGP updated to version 1.1 with previous version 1.0 dated 2015-07-23

Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>

Diff between FastGP versions 1.0 dated 2015-07-23 and 1.1 dated 2015-07-27

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Package cymruservices updated to version 0.1.1 with previous version 0.1.0 dated 2015-07-23

Title: Query Team Cymru IP Address, Autonomous System Number (ASN), Border Gateway Protocol (BGP), Bogon and Malware Hash Data Services
Description: A toolkit for querying Team Cymru <http://team-cymru.org> IP address, Autonomous System Number (ASN), Border Gateway Protocol (BGP), Bogon and Malware Hash Data Services.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>

Diff between cymruservices versions 0.1.0 dated 2015-07-23 and 0.1.1 dated 2015-07-27

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Package credule updated to version 0.1.2 with previous version 0.1 dated 2015-07-25

Title: Credit Default Swap Functions
Description: One function to bootstrap a credit curve from market quotes (Credit Default Swap spreads) and another function to price Credit Default Swaps from a credit curve.
Author: Bertrand Le Nezet [cre, aut, cph], Richard Brent [ctb, cph], John Burkardt [ctb, cph]
Maintainer: Bertrand Le Nezet <bertrand.lenezet@gmail.com>

Diff between credule versions 0.1 dated 2015-07-25 and 0.1.2 dated 2015-07-27

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Package cpm updated to version 2.2 with previous version 2.1 dated 2015-07-12

Title: Sequential and Batch Change Detection Using Parametric and Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>

Diff between cpm versions 2.1 dated 2015-07-12 and 2.2 dated 2015-07-27

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Package BOIN updated to version 1.2 with previous version 1.1 dated 2015-02-15

Title: Bayesian Optimal Interval Design for Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

Diff between BOIN versions 1.1 dated 2015-02-15 and 1.2 dated 2015-07-27

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Package bayesSurv updated to version 2.6 with previous version 2.4 dated 2015-02-05

Title: Bayesian Survival Regression with Flexible Error and Random Effects Distributions
Description: Contains Bayesian implementations of Mixed-Effects Accelerated Failure Time (MEAFT) models for censored data. Those can be not only right-censored but also interval-censored, doubly-interval-censored or misclassified interval-censored.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between bayesSurv versions 2.4 dated 2015-02-05 and 2.6 dated 2015-07-27

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New package spectrino with initial version 1.6.0
Package: spectrino
Type: Package
Title: Spectra Visualization, Organizer and Data Preparation
Version: 1.6.0
Date: 2015-07-27
Author: Teodor Krastev <spectrino@sicyon.com>
Maintainer: Teodor Krastev <spectrino@sicyon.com>
Description: Spectra visualization, organizer and data preparation from within R or stand-alone. Binary (application) part is installed separately by running spnInstallApp() immediately after installing the package.
License: GPL (>= 2)
OS_type: windows
Depends: R (>= 3.0.0)
Imports: utils, httpuv, jsonlite
LazyLoad: yes
LazyData: yes
URL: http://www.spectrino.com
BuildKeepEmpty: yes
Packaged: 2015-07-27 12:18:37 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-27 23:02:14

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New package qrage with initial version 1.0
Package: qrage
Type: Package
Title: Tools that Create D3 JavaScript Force Directed Graph from R
Version: 1.0
Date: 2015-07-27
Authors@R: c( person("\"Shingo Yamamoto (gloops, Inc.)\"",role=c("aut","cre"),email="si.yamamoto@gloops.com") ,person("RStudio, Inc.", role = "cph") ,person("Michael", "Bostock", role = c("ctb", "cph"), comment = "D3.js library") ,person(family = "jQuery Foundation", role = "cph",comment = "jQuery library and jQuery UI library") ,person(family = "jQuery contributors", role=c("ctb","cph"), comment= "jQuery library; authors listed in inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt") ,person(family = "jQuery UI contributors", role = c("ctb", "cph"),comment = "jQuery UI library; authors listed in inst/htmlwidgets/lib/jquery-ui/AUTHORS.txt") )
Author: "Shingo Yamamoto (gloops, Inc.)" [aut, cre], RStudio, Inc. [cph], Michael Bostock [ctb, cph] (D3.js library), jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/htmlwidgets/lib/jquery-ui/AUTHORS.txt)
Maintainer: "Shingo Yamamoto (gloops, Inc.)" <si.yamamoto@gloops.com>
Description: Tools that create D3 JavaScript force directed graph from R. D3 JavaScript was created by Michael Bostock. See http://d3js.org/ and, more specifically for Force Directed Graph https://github.com/mbostock/d3/wiki/Force-Layout.
License: MIT + file LICENSE
Imports: htmlwidgets
Suggests: shiny
NeedsCompilation: no
Packaged: 2015-07-27 03:03:09 UTC; si.yamamoto
Repository: CRAN
Date/Publication: 2015-07-27 23:08:07

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New package muRL with initial version 0.1-10
Package: muRL
Type: Package
Title: Mailmerge using R, LaTeX, and the Web
Version: 0.1-10
Date: 2015-07-27
Author: Ryan T. Moore <rtm@american.edu> and Andrew Reeves <reeves@wustl.edu>
Maintainer: Ryan T. Moore <rtm@american.edu>
Depends: utils, maps
Imports: graphics
Description: Provides mailmerge methods for reading spreadsheets of addresses and other relevant information to create standardized but customizable letters. Provides a method for mapping US ZIP codes, including those of letter recipients. Provides a method for parsing and processing html code from online job postings of the American Political Science Association.
License: GPL-2 | file LICENSE
URL: http://nw18.american.edu/~rtm/software.muRL.htm
LazyLoad: yes
NeedsCompilation: no
Packaged: 2015-07-27 19:51:16 UTC; rtm
Repository: CRAN
Date/Publication: 2015-07-27 22:56:23

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Package sitar updated to version 1.0.3 with previous version 1.0.2 dated 2015-04-21

Title: Super Imposition by Translation and Rotation Growth Curve Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>

Diff between sitar versions 1.0.2 dated 2015-04-21 and 1.0.3 dated 2015-07-27

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Package DiscreteLaplace updated to version 1.1 with previous version 1.0 dated 2012-02-02

Title: Discrete Laplace Distributions
Description: Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
Author: Alessandro Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo <riccardo.arner@libero.it>
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>

Diff between DiscreteLaplace versions 1.0 dated 2012-02-02 and 1.1 dated 2015-07-27

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Package changepoint updated to version 2.0.1 with previous version 1.1.5 dated 2014-06-25

Title: An R Package for Changepoint Analysis
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean, cpt.var, cpt.meanvar functions should be your first point of call.
Author: Rebecca Killick [aut, cre], Kaylea Haynes [aut], Idris Eckley [aut], Paul Fearnhead [ctb], Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>

Diff between changepoint versions 1.1.5 dated 2014-06-25 and 2.0.1 dated 2015-07-27

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Package alineR updated to version 1.1 with previous version 1.0 dated 2015-07-10

Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre], Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>

Diff between alineR versions 1.0 dated 2015-07-10 and 1.1 dated 2015-07-27

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Package rbamtools updated to version 2.12.3 with previous version 2.12.2 dated 2015-07-16

Title: An R Package for Reading and Writing BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Diff between rbamtools versions 2.12.2 dated 2015-07-16 and 2.12.3 dated 2015-07-27

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New package OptGS with initial version 1.0
Package: OptGS
Type: Package
Title: Near-Optimal and Balanced Group-Sequential Designs for Clinical Trials with Continuous Outcomes
Version: 1.0
Date: 2015-07-27
Authors@R: c(person("James", "Wason", email = "james.wason@mrc-bsu.cam.ac.uk", role = c("aut", "cre")),person("John","Burkardt",role="ctb"))
Maintainer: James Wason <james.wason@mrc-bsu.cam.ac.uk>
Description: Functions to find near-optimal multi-stage designs for continuous outcomes.
License: GPL-2
Packaged: 2015-07-27 13:35:28 UTC; jamesw
NeedsCompilation: yes
Author: James Wason [aut, cre], John Burkardt [ctb]
Repository: CRAN
Date/Publication: 2015-07-27 15:40:26

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Package MXM updated to version 0.4.2 with previous version 0.4.1 dated 2015-07-09

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>

Diff between MXM versions 0.4.1 dated 2015-07-09 and 0.4.2 dated 2015-07-27

 DESCRIPTION         |    8 ++++----
 MD5                 |   12 ++++++------
 NAMESPACE           |    2 +-
 R/SES.R             |    1 +
 R/censIndLR.R       |   33 +++++++++++++++++----------------
 R/testIndLogistic.R |    6 +++++-
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 7 files changed, 36 insertions(+), 30 deletions(-)

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New package lazyWeave with initial version 3.0.0
Package: lazyWeave
Type: Package
Title: LaTeX Wrappers for R Users
Version: 3.0.0
Date: 2015-07-27
Author: Benjamin Nutter
Maintainer: Benjamin Nutter <nutter@battelle.org>
Description: Provides the functionality to write LaTeX code from within R without having to learn LaTeX. Functionality also exists to create HTML and Markdown code. While the functionality still exists to write complete documents with lazyWeave, it is generally easier to do so with with markdown and knitr. lazyWeave's main strength now is the ability to design custom and complex tables for reporting results.
License: GPL
LazyLoad: yes
Depends: R (>= 2.10.0)
Imports: Hmisc (>= 3.14-6)
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-07-27 13:01:23 UTC; bnutter
Repository: CRAN
Date/Publication: 2015-07-27 15:05:40

More information about lazyWeave at CRAN
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New package rddtools with initial version 0.4.0
Package: rddtools
Version: 0.4.0
Title: Toolbox for Regression Discontinuity Design ('RDD')
Description: Set of functions for Regression Discontinuity Design ('RDD'), for data visualisation, estimation and testing.
Authors@R: c( person("Matthieu", "Stigler", role = "aut"), person("Bastiaan", "Quast", email = "bquast@gmail.com", role = c("aut", "cre") ) )
Maintainer: Bastiaan Quast <bquast@gmail.com>
Imports: KernSmooth, ggplot2, rdd, sandwich, lmtest, Formula, locpol, methods
Depends: AER, np
Suggests: stats4, car, knitr, testthat
License: GPL (>= 2)
URL: https://github.com/bquast/RDDtools
BugReports: https://github.com/bquast/RDDtools/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-07-27 11:01:48 UTC; quast2
Author: Matthieu Stigler [aut], Bastiaan Quast [aut, cre]
Repository: CRAN
Date/Publication: 2015-07-27 13:32:08

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Package RGA updated to version 0.2.3 with previous version 0.2.2 dated 2015-06-14

Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>

Diff between RGA versions 0.2.2 dated 2015-06-14 and 0.2.3 dated 2015-07-27

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 63 files changed, 525 insertions(+), 336 deletions(-)

More information about RGA at CRAN
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New package momr with initial version 1.1
Package: momr
Title: Mining Metaomics Data (MetaOMineR)
Version: 1.1
Date: 2015-07-24
Author: Edi Prifti, Emmanuelle Le Chatelier
Maintainer: Edi Prifti <edi.prifti@gmail.com>
Description: 'MetaOMineR' suite is a set of R packages that offers many functions and modules needed for the analyses of quantitative metagenomics data. 'momr' is the core package and contains routines for biomarker identification and exploration. Developed since the beginning of field, 'momr' has evolved and is structured around the different modules such as preprocessing, analysis, vizualisation, etc. See package help for more information.
License: Artistic-2.0
Depends: R (>= 2.10)
Imports: Hmisc, gplots, nortest
Collate: 'normalization.R' 'downsizing.R' 'querries.R' 'filtering.R' 'visualization.R' 'analyses.R' 'data.R' 'mapreduce.R'
LazyLoad: yes
License_restricts_use: yes
Packaged: 2015-07-27 10:20:05 UTC; eprifti
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-27 12:42:14

More information about momr at CRAN
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Package adagio updated to version 0.6.1 with previous version 0.5.9 dated 2013-09-28

Title: Discrete and Global Optimization Routines
Description: The R package 'adagio' will provide methods and algorithms for discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

Diff between adagio versions 0.5.9 dated 2013-09-28 and 0.6.1 dated 2015-07-27

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 17 files changed, 103 insertions(+), 113 deletions(-)

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Package warbleR updated to version 1.0.2 with previous version 1.0.1 dated 2015-07-24

Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>

Diff between warbleR versions 1.0.1 dated 2015-07-24 and 1.0.2 dated 2015-07-27

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 53 files changed, 574 insertions(+), 464 deletions(-)

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Package rtop updated to version 0.5-5 with previous version 0.3-45 dated 2014-02-10

Title: Interpolation of Data with Variable Spatial Support
Description: Geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>

Diff between rtop versions 0.3-45 dated 2014-02-10 and 0.5-5 dated 2015-07-27

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Package rngWELL updated to version 0.10-4 with previous version 0.10-3 dated 2014-07-25

Title: Toolbox for WELL Random Number Generators
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky <savicky@cs.cas.cz>.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

Diff between rngWELL versions 0.10-3 dated 2014-07-25 and 0.10-4 dated 2015-07-27

 DESCRIPTION  |   13 ++++++-------
 LICENSE      |    2 +-
 MD5          |    6 +++---
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 4 files changed, 38 insertions(+), 35 deletions(-)

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Package nor1mix updated to version 1.2-1 with previous version 1.2-0 dated 2014-09-02

Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Now fitting to data by ML (Maximum Likelihood) or EM estimation.
Author: Martin Mächler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

Diff between nor1mix versions 1.2-0 dated 2014-09-02 and 1.2-1 dated 2015-07-27

 ChangeLog         |    5 +++++
 DESCRIPTION       |    8 ++++----
 MD5               |   10 +++++-----
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 6 files changed, 24 insertions(+), 16 deletions(-)

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Package mongolite updated to version 0.5 with previous version 0.4 dated 2015-06-10

Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver. Includes support for aggregation, indexing, map-reduce, streaming, 'TLS' encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between mongolite versions 0.4 dated 2015-06-10 and 0.5 dated 2015-07-27

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Package HiveR updated to version 0.2.44 with previous version 0.2-28 dated 2015-01-21

Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre], Vesna Memisevic [ctb], Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

Diff between HiveR versions 0.2-28 dated 2015-01-21 and 0.2.44 dated 2015-07-27

 DESCRIPTION          |   14 -
 MD5                  |   35 ++--
 NAMESPACE            |    8 
 NEWS                 |  421 +++++++++++++++++++++------------------------------
 R/adj2HPD.R          |    2 
 R/animateHive.R      |   19 +-
 R/drawHiveSpline.R   |   10 -
 R/manipAxis.R        |    7 
 R/plot3dHive.R       |  105 +++++++-----
 R/plotHive.R         |   76 ++++++---
 R/ranHiveData.R      |   10 -
 R/rcsr.R             |    2 
 R/sumHPD.R           |   10 -
 build/vignette.rds   |binary
 inst/doc/HiveR.pdf   |binary
 man/HidingAnAxis.Rd  |only
 man/HiveR-package.Rd |   12 -
 man/ranHiveData.Rd   |    2 
 man/rcsr.Rd          |    2 
 19 files changed, 369 insertions(+), 366 deletions(-)

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Package dcGOR updated to version 1.0.6 with previous version 1.0.5 dated 2015-07-20

Title: Analysis of Ontologies and Protein Domain Annotations
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between dcGOR versions 1.0.5 dated 2015-07-20 and 1.0.6 dated 2015-07-27

 DESCRIPTION                |   12 ++--
 MD5                        |   58 +++++++++----------
 R/dcAlgo.r                 |    4 -
 R/dcAlgoPredict.r          |    4 -
 R/dcAlgoPredictGenome.r    |    4 -
 R/dcAlgoPredictMain.r      |    4 -
 R/dcAlgoPredictPR.r        |    4 -
 R/dcAlgoPropagate.r        |    4 -
 R/dcEnrichment.r           |    2 
 R/dcList2Matrix.r          |    2 
 R/dcNaivePredict.r         |    4 -
 R/dcRDataLoader.r          |  135 ++++++++++++++++++++++++++++++++++++---------
 R/dcRWRpredict.r           |    4 -
 R/dcSparseMatrix.r         |    2 
 inst/NEWS                  |    8 ++
 inst/staticdocs/README.md  |    2 
 man/dcAlgo.Rd              |   17 +----
 man/dcAlgoPredict.Rd       |   17 +----
 man/dcAlgoPredictGenome.Rd |   17 +----
 man/dcAlgoPredictMain.Rd   |   17 +----
 man/dcAlgoPredictPR.Rd     |   17 +----
 man/dcAlgoPropagate.Rd     |   17 +----
 man/dcEnrichment.Rd        |   14 ----
 man/dcList2Matrix.Rd       |    2 
 man/dcNaivePredict.Rd      |   17 +----
 man/dcRDataLoader.Rd       |   24 ++++----
 man/dcRWRpredict.Rd        |   17 +----
 man/dcSparseMatrix.Rd      |    4 -
 man/onto.DO.Rd             |    2 
 man/onto.MP.Rd             |    2 
 30 files changed, 218 insertions(+), 219 deletions(-)

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Package d3heatmap updated to version 0.6.1 with previous version 0.6.0 dated 2015-06-23

Title: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'
Description: Create interactive heat maps that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a cell to show details, drag a rectangle to zoom, and click row/column labels to highlight.
Author: Joe Cheng [aut, cre], Tal Galili [aut], RStudio, Inc. [cph], Michael Bostock [ctb, cph] (D3.js library), Justin Palmer [ctb, cph] (d3.tip library)
Maintainer: Joe Cheng <joe@rstudio.com>

Diff between d3heatmap versions 0.6.0 dated 2015-06-23 and 0.6.1 dated 2015-07-27

 DESCRIPTION                                   |   10 
 MD5                                           |   18 
 NAMESPACE                                     |   10 
 NEWS                                          |    7 
 R/d3heatmap.R                                 |    6 
 README.md                                     |   12 
 inst/doc/Introduction.html                    |   35 -
 inst/htmlwidgets/lib/d3heatmapcore/heatmap.js |   15 
 tests/smoketest.R                             |    4 
 tests/smoketest.Rout.save                     |  686 +++++++++++++-------------
 10 files changed, 415 insertions(+), 388 deletions(-)

More information about d3heatmap at CRAN
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