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 Sb [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 Mchler
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 
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 R/adj2HPD.R          |    2 
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 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 ++--
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 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 
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 tests/smoketest.R                             |    4 
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 10 files changed, 415 insertions(+), 388 deletions(-)

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Sun, 26 Jul 2015

Package flam updated to version 3.0 with previous version 2.0 dated 2015-06-25

Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ajpete@uw.edu>

Diff between flam versions 2.0 dated 2015-06-25 and 3.0 dated 2015-07-26

 DESCRIPTION         |   10 +++++-----
 MD5                 |   14 +++++++-------
 NAMESPACE           |    3 +++
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 R/flam_fcns.R       |    4 ++--
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 8 files changed, 39 insertions(+), 41 deletions(-)

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Package mixlm updated to version 1.0.9.2 with previous version 1.0.8.5 dated 2015-03-11

Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [ctb], R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between mixlm versions 1.0.8.5 dated 2015-03-11 and 1.0.9.2 dated 2015-07-26

 DESCRIPTION    |   10 ++++------
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 6 files changed, 31 insertions(+), 43 deletions(-)

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Package Mediana updated to version 1.0.1 with previous version 1.0 dated 2015-07-26

Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based on the Clinical Scenario Evaluation (CSE) approach. The package supports a broad class of data models (including clinical trials with continuous, binary, survival-type and count-type endpoints as well as multivariate outcomes that are based on combinations of different endpoints), analysis strategies and commonly used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>

Diff between Mediana versions 1.0 dated 2015-07-26 and 1.0.1 dated 2015-07-26

 DESCRIPTION            |    9 +++++----
 MD5                    |   10 +++++-----
 R/Mediana.R            |   10 +++++-----
 man/Criterion.Rd       |    2 +-
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 man/SampleSize.Rd      |    2 +-
 6 files changed, 19 insertions(+), 18 deletions(-)

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Package lsmeans updated to version 2.19 with previous version 2.18 dated 2015-06-01

Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth <russell-lenth@uiowa.edu>

Diff between lsmeans versions 2.18 dated 2015-06-01 and 2.19 dated 2015-07-26

 DESCRIPTION                 |   13 ++-
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 vignettes/using-lsmeans.rnw |    2 
 28 files changed, 338 insertions(+), 157 deletions(-)

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New package landsat8 with initial version 0.1-9
Package: landsat8
Type: Package
Title: Landsat 8 Imagery Rescaled to Reflectance, Radiance and/or Temperature
Version: 0.1-9
Date: 2015-07-21
Author: Alexandre dos Santos
Maintainer: Alexandre dos Santos <alexandre.santos@cas.ifmt.edu.br>
Description: Functions for converted Landsat 8 multispectral satellite imagery rescaled to the top of atmosphere (TOA) reflectance, radiance and/or at satellite brightness temperature using radiometric rescaling coefficients provided in the metadata file (MTL file).
Imports: rgdal, sp
Depends: R (>= 3.1.2)
License: GPL-2
LazyData: TRUE
Packaged: 2015-07-26 19:10:40 UTC; ASANTOS
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-26 23:10:31

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New package rstpm2 with initial version 1.2.2
Package: rstpm2
Type: Package
Title: Flexible Link-Based Survival Models
Authors@R: c(person("Mark", "Clements", role = c("aut", "cre"), email = "mark.clements@ki.se"), person("Xing-Rong", "Liu", role = "aut", email = "xingrong.liu@ki.se"), person("Paul", "Lambert", role = "ctb", email="pl4@leicester.ac.uk"))
Version: 1.2.2
Date: 2015-07-12
Depends: R (>= 2.10), methods, survival, splines
Imports: graphics, Rcpp (>= 0.10.2), numDeriv, stats, mgcv, bbmle (>= 1.0.3)
Suggests: RUnit, gaussquad
LinkingTo: Rcpp,RcppArmadillo
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Description: R implementation of Stata's stpm2 function (flexible link-based survival models), with extensions to different smoothers and penalised models.
URL: http://github.com/mclements/rstpm2
BugReports: http://github.com/mclements/rstpm2/issues
License: GPL-2 | GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2015-07-26 09:13:35 UTC; marcle
Repository: CRAN
Date/Publication: 2015-07-26 18:57:30

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Package COMBIA updated to version 1.0-4 with previous version 1.0-3 dated 2015-07-25

Title: Synergy/Antagonism Analyses of Drug Combinations
Description: A comprehensive synergy/antagonism analyses of drug combinations with quality graphics and data. The analyses can be performed by Bliss independence and Loewe additivity models. COMBIA provides improved statistical analysis and makes only very weak assumption of data variability while calculating bootstrap intervals (BIs). Finally, package saves analyzed data, 2D and 3D plots ready to use in research publications. COMBIA does not require manual data entry. Data can be directly input from wetlab experimental platforms for example fluostar, automated robots etc. One needs to call a single function only to perform all analysis (examples are provided with sample data).
Author: Muhammad Kashif
Maintainer: Muhammad Kashif <Muhammad.Kashif@medsci.uu.se>

Diff between COMBIA versions 1.0-3 dated 2015-07-25 and 1.0-4 dated 2015-07-26

 DESCRIPTION                                |    6 ++--
 MD5                                        |   24 ++++++++--------
 R/COMBIA.R                                 |   42 +++++++++++++----------------
 inst/raw/FluoOptima_384_2014-03-28test.xls |binary
 inst/raw/testData.xls                      |binary
 man/applyLoewe.Rd                          |    8 ++---
 man/calculateSynergy.Rd                    |    2 -
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 man/readMacSynergyValues.Rd                |    2 -
 man/readOtherValues.Rd                     |    4 +-
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 man/synAntPlot.Rd                          |    2 -
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 13 files changed, 51 insertions(+), 53 deletions(-)

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New package mHG with initial version 1.0
Package: mHG
Type: Package
Title: Minimum-Hypergeometric Test
Version: 1.0
Date: 2015-07-22
Author: Kobi Perl
Maintainer: Kobi Perl <kobipe3@gmail.com>
Description: Runs a minimum-hypergeometric (mHG) test as described in: Eden, E. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. Haifa.
License: GPL-2
Depends: methods
Suggests: testthat
Packaged: 2015-07-26 06:41:10 UTC; kobiperl
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-26 09:23:57

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New package tglm with initial version 1.0
Package: tglm
Type: Package
Title: Binary Regressions under Independent Student-t Priors
Version: 1.0
Date: 2015-07-24
Author: Yingbo Li
Maintainer: Yingbo Li <ybli@clemson.edu>
Description: Use Gibbs sampler with Polya-Gamma data augmentation to fit logistic and probit regression under independent Student-t priors (including Cauchy priors and normal priors as special cases).
License: GPL (>= 2)
Depends: R (>= 2.14.0)
Imports: BayesLogit, mvtnorm, coda, truncnorm
Packaged: 2015-07-26 03:10:34 UTC; ybli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-26 09:11:35

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Package RcppZiggurat updated to version 0.1.3 with previous version 0.1.2 dated 2014-01-26

Title: 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations
Description: The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (JSS, 2000), has been improved upon a few times starting with Leong et al (JSS, 2005). This package provides an aggregation in order to compare different implementations. The goal is to provide an 'faster but good enough' alternative for use with R and C++ code. The package is still in an early state. Unless you know what you are doing, sticking with the generators provided by R may be a good idea as these have been extremely diligently tested.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppZiggurat versions 0.1.2 dated 2014-01-26 and 0.1.3 dated 2015-07-26

 ChangeLog                       |   49 +++++
 DESCRIPTION                     |   14 -
 MD5                             |   56 +++---
 NAMESPACE                       |    7 
 R/RcppExports.R                 |    4 
 README.md                       |   18 +-
 build/vignette.rds              |binary
 demo/benchmark.R                |    6 
 inst/NEWS.Rd                    |   19 ++
 inst/doc/RcppZiggurat.R         |   14 +
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 inst/include/Ziggurat.h         |   37 ++--
 inst/include/ZigguratLZLLV.h    |   12 -
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 inst/include/ZigguratV1.h       |   33 +--
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 src/Makevars                    |    2 
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New package packcircles with initial version 0.1.1
Package: packcircles
Type: Package
Title: Circle Packing
Version: 0.1.1
Date: 2015-07-22
Authors@R: c( person("Michael", "Bedward", role = c("aut", "cre"), email = "michael.bedward@gmail.com"), person("David", "Eppstein", role = "aut", email = "david.eppstein@gmail.com", comment = "Original author of Python code for graph-based circle packing ported to C++ for this package"))
Description: Simple algorithm to arrange non-overlapping circles within a rectangle.
License: MIT + file LICENSE
URL: https://github.com/mbedward/packcircles
Imports: Rcpp (>= 0.11.5)
Suggests: ggplot2, gridExtra, knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-07-26 03:49:55 UTC; mbedward
Author: Michael Bedward [aut, cre], David Eppstein [aut] (Original author of Python code for graph-based circle packing ported to C++ for this package)
Maintainer: Michael Bedward <michael.bedward@gmail.com>
Repository: CRAN
Date/Publication: 2015-07-26 09:11:33

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Package mvSLOUCH updated to version 1.2 with previous version 1.1.5 dated 2015-01-21

Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>

Diff between mvSLOUCH versions 1.1.5 dated 2015-01-21 and 1.2 dated 2015-07-26

 DESCRIPTION                        |   11 +++--
 MD5                                |   44 ++++++++++++----------
 NAMESPACE                          |    8 ++--
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 25 files changed, 329 insertions(+), 242 deletions(-)

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New package Mediana with initial version 1.0
Package: Mediana
Type: Package
Title: Clinical Trial Simulations
Version: 1.0
Date: 2015-07-25
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Description: Provides a general framework for clinical trial simulations based on the Clinical Scenario Evaluation (CSE) approach. The package supports a broad class of data models (including clinical trials with continuous, binary, survival-type and count-type endpoints as well as multivariate outcomes that are based on combinations of different endpoints), analysis strategies and commonly used evaluation criteria.
Imports: doParallel, doRNG, foreach, MASS, mvtnorm, ReporteRs, stats, survival, utils
License: GPL-2
URL: http://biopharmnet.com/mediana
NeedsCompilation: no
Packaged: 2015-07-25 22:00:59 UTC; Gautier
Repository: CRAN
Date/Publication: 2015-07-26 09:11:19

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Package checkmate updated to version 1.6.2 with previous version 1.6.1 dated 2015-07-17

Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang <michellang@gmail.com>, Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>

Diff between checkmate versions 1.6.1 dated 2015-07-17 and 1.6.2 dated 2015-07-26

 DESCRIPTION             |   10 +++---
 MD5                     |   20 ++++++------
 NAMESPACE               |    2 -
 NEWS                    |    8 ++++
 R/helper.r              |    6 ++-
 R/zzz.r                 |    2 -
 build/vignette.rds      |binary
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 src/any_nan.c           |    4 --
 src/checks.c            |    2 -
 src/is_integerish.c     |    4 +-
 11 files changed, 60 insertions(+), 76 deletions(-)

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Sat, 25 Jul 2015

New package credule with initial version 0.1
Package: credule
Version: 0.1
Date: 2015-07-16
Title: Credit Default Swap Functions
Authors@R: c(person("Bertrand", "Le Nezet", role = c("cre","ctb", "cph"), email = "bertrand.lenezet@gmail.com" ))
Maintainer: Bertrand Le Nezet <bertrand.lenezet@gmail.com>
Depends: R (>= 2.14.1)
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.
License: MIT + file LICENSE
NeedsCompilation: yes
Packaged: 2015-07-25 16:24:10 UTC; pc
Author: Bertrand Le Nezet [cre, ctb, cph]
Repository: CRAN
Date/Publication: 2015-07-25 23:13:39

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Package soilwater updated to version 1.0.2 with previous version 1.0.1 dated 2012-12-04

Title: Implementation of Parametric Formulas for Soil Water Retention or Conductivity Curve
Description: It is a set of R implementations of parametric formulas of soil water retention or conductivity curve. At the moment, only Van Genuchten (for soil water retention curve) and Mualem (for hydraulic conductivity) were implemented. See reference \url{http://en.wikipedia.org/wiki/Water_retention_curve}.
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>

Diff between soilwater versions 1.0.1 dated 2012-12-04 and 1.0.2 dated 2015-07-25

 soilwater-1.0.1/soilwater/LICENSE                             |only
 soilwater-1.0.1/soilwater/R/soilwater-package.R               |only
 soilwater-1.0.1/soilwater/man/soilwater-package.Rd            |only
 soilwater-1.0.2/soilwater/DESCRIPTION                         |   29 +--
 soilwater-1.0.2/soilwater/MD5                                 |   21 +-
 soilwater-1.0.2/soilwater/NAMESPACE                           |    3 
 soilwater-1.0.2/soilwater/R/additional.water.table.recharge.R |only
 soilwater-1.0.2/soilwater/R/hydraulic_diffusivity.R           |   43 +++-
 soilwater-1.0.2/soilwater/R/volume.R                          |    4 
 soilwater-1.0.2/soilwater/README.md                           |only
 soilwater-1.0.2/soilwater/inst/doc/example/SWRC.R             |    6 
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 soilwater-1.0.2/soilwater/man/hydraulic_diffusivity.Rd        |   92 +++++-----
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 15 files changed, 129 insertions(+), 103 deletions(-)

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New package rgeolocate with initial version 0.4.1
Package: rgeolocate
Type: Package
Title: IP Address Geolocation
Version: 0.4.1
Date: 2015-07-25
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Copyright: MaxMind, Inc. for the underlying libmaxmminddb library, and the package authors for all other content.
Description: Connectors to online and offline sources for taking IP addresses and geolocating them to country, city, timezone and other geographic ranges. For individual connectors, see the package index.
License: Apache License (== 2.0)
BugReports: https://github.com/ironholds/rgeolocate/issues
LinkingTo: Rcpp
Imports: Rcpp, httr
Suggests: testthat, knitr, iptools
VignetteBuilder: knitr
Packaged: 2015-07-25 20:18:23 UTC; ironholds
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-25 23:05:39

More information about rgeolocate at CRAN
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Package glmvsd updated to version 1.3 with previous version 1.2 dated 2015-02-13

Title: Variable Selection Deviation Measures and Instability Tests for High-Dimensional Generalized Linear Models
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan <nanx0006@gmail.com>, Yi Yang <yiyang@umn.edu>, Yuhong Yang <yyang@stat.umn.edu>, Chenglong Ye <yexxx323@umn.edu>
Maintainer: Yi Yang <yiyang@umn.edu>

Diff between glmvsd versions 1.2 dated 2015-02-13 and 1.3 dated 2015-07-25

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Package FCNN4R updated to version 0.3.4 with previous version 0.3.3 dated 2015-07-21

Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines from the FCNN C++ library. FCNN is based on a completely new Artificial Neural Network representation that offers unmatched efficiency, modularity, and extensibility. FCNN4R provides standard teaching (backpropagation, Rprop) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon), but it is first and foremost an efficient computational engine. Users can easily implement their algorithms by taking advantage of fast gradient computing routines, as well as network reconstruction functionality (removing weights and redundant neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>

Diff between FCNN4R versions 0.3.3 dated 2015-07-21 and 0.3.4 dated 2015-07-25

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Package TAM updated to version 1.10-0 with previous version 1.9-0 dated 2015-06-30

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between TAM versions 1.9-0 dated 2015-06-30 and 1.10-0 dated 2015-07-25

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Package nonlinearTseries updated to version 0.2.3 with previous version 0.2.2 dated 2015-06-03

Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits the computation of the most-used nonlinear statistics/algorithms including generalized correlation dimension, information dimension, largest Lyapunov exponent, sample entropy and Recurrence Quantification Analysis (RQA), among others. Basic routines for surrogate data testing are also included. Part of this work was based on the book "Nonlinear time series analysis" by Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre], Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantinoantonio.garcia@usc.es>

Diff between nonlinearTseries versions 0.2.2 dated 2015-06-03 and 0.2.3 dated 2015-07-25

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 nonlinearTseries-0.2.3/nonlinearTseries/src/kd_dump.cpp                           |   11 +-
 nonlinearTseries-0.2.3/nonlinearTseries/src/kd_split.cpp                          |   22 +----
 nonlinearTseries-0.2.3/nonlinearTseries/vignettes/nonlinearTseries_quickstart.Rmd |   25 ++---
 25 files changed, 163 insertions(+), 139 deletions(-)

More information about nonlinearTseries at CRAN
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Package VideoComparison updated to version 0.15 with previous version 0.11 dated 2014-07-09

Title: Video Comparison Tool
Description: It will take the vectors of motion for two videos (coming from a variant of shotdetect code allowing to store detailed motion vectors in JSON format, for instance) and it will look for comparing taking out the common chunk. Then, provided you have some image's hashes it will compare their signature in order to make up the decision about chunk similarity of two video files. ShotDetect is a free software which detects shots and scenes from a video (http://johmathe.name/shotdetect.html).
Author: Silvia Espinosa, Joaquin Ordieres, Antonio Bello, Jose Maria Perez
Maintainer: Joaquin Ordieres <j.ordieres@upm.es>

Diff between VideoComparison versions 0.11 dated 2014-07-09 and 0.15 dated 2015-07-25

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More information about VideoComparison at CRAN
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Package Rcpp updated to version 0.12.0 with previous version 0.11.6 dated 2015-05-01

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rcpp versions 0.11.6 dated 2015-05-01 and 0.12.0 dated 2015-07-25

 ChangeLog                                                     |  127 ++++
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Package RandomFields updated to version 3.1.1 with previous version 3.1.0 dated 2015-07-24

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.1.0 dated 2015-07-24 and 3.1.1 dated 2015-07-25

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Package equivalence updated to version 0.7.0 with previous version 0.6.0 dated 2014-06-06

Title: Provides Tests and Graphics for Assessing Tests of Equivalence
Description: Provides statistical tests and graphics for assessing tests of equivalence. Such tests have similarity as the alternative hypothesis instead of the null. Sample data sets are included.
Author: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>
Maintainer: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>

Diff between equivalence versions 0.6.0 dated 2014-06-06 and 0.7.0 dated 2015-07-25

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New package COMBIA with initial version 1.0-3
Encoding: UTF-8
Package: COMBIA
Type: Package
Title: Synergy/Antagonism Analyses of Drug Combinations
Version: 1.0-3
Date: 2015-07-24
Author: Muhammad Kashif
Maintainer: Muhammad Kashif <Muhammad.Kashif@medsci.uu.se>
Description: A comprehensive synergy/antagonism analyses of drug combinations with quality graphics and data. The analyses can be performed by Bliss independence and Loewe additivity models. COMBIA provides improved statistical analysis and makes only very weak assumption of data variability while calculating bootstrap intervals (BIs). Finally, package saves analyzed data, 2D and 3D plots ready to use in research publications. COMBIA does not require manual data entry. Data can be directly input from wetlab experimental platforms for example fluostar, automated robots etc. One needs to call a single function only to perform all analysis (examples are provided with sample data).
Depends: hash, gdata, lattice, latticeExtra, oro.nifti
Imports: grDevices, stats, utils
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2015-07-25 06:07:42 UTC; dawood
Repository: CRAN
Date/Publication: 2015-07-25 11:38:23

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Fri, 24 Jul 2015

Package dynsim updated to version 1.2 with previous version 1.0 dated 2014-08-13

Title: Dynamic Simulations of Autoregressive Relationships
Description: Dynamic simulations and graphical depictions of autoregressive relationships.
Author: Christopher Gandrud [aut, cre], Laron K. Williams [aut], Guy D. Whitten [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

Diff between dynsim versions 1.0 dated 2014-08-13 and 1.2 dated 2015-07-24

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More information about dynsim at CRAN
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Package ddalpha updated to version 1.1.3.1 with previous version 1.1.3 dated 2015-07-23

Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut], Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>

Diff between ddalpha versions 1.1.3 dated 2015-07-23 and 1.1.3.1 dated 2015-07-24

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

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New package RKlout with initial version 1.0
Package: RKlout
Type: Package
Title: Fetch Klout Scores for Twitter Users
Version: 1.0
Date: 2015-07-22
Author: Binayak Goswami
Maintainer: Binayak Goswami <bnayok@gmail.com>
Description: An interface of R to Klout API v2. It fetches Klout Score for a Twitter Username/handle in real time. Klout is a website and mobile app that uses social media analytics to rank its users according to online social influence via the "Klout Score", which is a numerical value between 1 and 100. In determining the user score, Klout measures the size of a user's social media network and correlates the content created to measure how other users interact with that content.
License: GPL-2
Imports: RCurl
Packaged: 2015-07-24 17:26:33 UTC; Ubuntu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-24 21:10:41

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Permanent link

Package quantmod updated to version 0.4-5 with previous version 0.4-4 dated 2015-03-08

Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, ctb], Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>

Diff between quantmod versions 0.4-4 dated 2015-03-08 and 0.4-5 dated 2015-07-24

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Package archdata updated to version 1.0 with previous version 0.1 dated 2014-07-15

Title: Example Datasets from Archaeological Research
Description: The archdata package provides several types of data that are typically used in archaeological research.
Author: David L. Carlson
Maintainer: David L. Carlson <dcarlson@tamu.edu>

Diff between archdata versions 0.1 dated 2014-07-15 and 1.0 dated 2015-07-24

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More information about archdata at CRAN
Permanent link

New package varian with initial version 0.2.1
Package: varian
Type: Package
Version: 0.2.1
Title: Variability Analysis in R
Description: Uses a Bayesian model to estimate the variability in a repeated measure outcome and use that as an outcome or a predictor in a second stage model.
Date: 2015-7-24
Author: Joshua F. Wiley [aut, cre], Elkhart Group Limited [cph]
Maintainer: Joshua F. Wiley <josh@elkhartgroup.com>
URL: https://github.com/ElkhartGroup/varian
BugReports: https://github.com/ElkhartGroup/varian/issues
Depends: R (>= 3.1.1), rstan (>= 2.7.0), ggplot2
Imports: stats, MASS, Formula, grid, gridExtra
Suggests: testthat
LazyLoad: yes
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2015-07-24 12:46:24 UTC; Joshua
Repository: CRAN
Date/Publication: 2015-07-24 18:21:42

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Permanent link

New package TransModel with initial version 1.0
Package: TransModel
Type: Package
Title: Fit Linear Transformation Models for Censored Data
Version: 1.0
Date: 2015-07-23
Author: Jie Zhou, Jiajia Zhang, Wenbin Lu
Maintainer: Jie Zhou <zhoujie02569@gmail.com>
Description: A unified estimation procedure for the analysis of censored data using linear transformation models.
License: GPL-2
Depends: stats,graphics,survival
Packaged: 2015-07-24 16:31:19 UTC; gazhou
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-24 19:05:32

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New package rotl with initial version 0.4.1
Package: rotl
Title: Interface to the 'Open Tree of Life' API
Version: 0.4.1
Authors@R: c( person("Francois", "Michonneau", role=c("aut", "cre"), email="francois.michonneau@gmail.com"), person("Joseph", "Brown", role="aut"), person("David", "Winter", role="aut"))
Description: An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
URL: https://github.com/ropensci/rotl
BugReports: https://github.com/ropensci/rotl/issues
Depends: R (>= 3.1.1)
Imports: httr, jsonlite, rncl (>= 0.6.0), ape
License: BSD_2_clause + file LICENSE
Suggests: knitr (>= 1.10.5), rmarkdown (>= 0.7), testthat, RNeXML, phylobase
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2015-07-24 14:37:18 UTC; francois
Author: Francois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Repository: CRAN
Date/Publication: 2015-07-24 18:21:38

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Package RandomFields updated to version 3.1.0 with previous version 3.0.62 dated 2015-02-03

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.0.62 dated 2015-02-03 and 3.1.0 dated 2015-07-24

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More information about RandomFields at CRAN
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Package pipe.design updated to version 0.3 with previous version 0.2 dated 2015-05-12

Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>

Diff between pipe.design versions 0.2 dated 2015-05-12 and 0.3 dated 2015-07-24

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More information about pipe.design at CRAN
Permanent link

Package phylobase updated to version 0.8.0 with previous version 0.6.8 dated 2014-03-20

Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package mombf updated to version 1.6.0 with previous version 1.5.9 dated 2014-11-11

Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>

Diff between mombf versions 1.5.9 dated 2014-11-11 and 1.6.0 dated 2015-07-24

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Package modMax updated to version 1.1 with previous version 1.0 dated 2015-02-18

Title: Community Structure Detection via Modularity Maximization
Description: The algorithms implemented here are used to detect the community structure of a network. These algorithms follow different approaches, but are all based on the concept of modularity maximization.
Author: Maria Schelling, Cang Hui
Maintainer: Maria Schelling <schelling.rmaintainer@vodafone.de>

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Package glmm updated to version 1.0.4 with previous version 1.0.3 dated 2015-04-28

Title: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson <christina@stat.umn.edu>

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Package MicSim updated to version 1.0.9 with previous version 1.0.8 dated 2015-03-05

Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>

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Package isotone updated to version 1.1-0 with previous version 1.0-2 dated 2014-09-10

Title: Active Set and Generalized PAVA for Isotone Optimization
Description: Contains two main functions: one for solving general isotone regression problems using the pool-adjacent-violators algorithm (PAVA); another one provides a framework for active set methods for isotone optimization problems with arbitrary order restrictions. Various types of loss functions are prespecified.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Kurt Hornik [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package aspect updated to version 1.0-4 with previous version 1.0-3 dated 2014-11-26

Title: A General Framework for Multivariate Analysis with Optimal Scaling
Description: Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
Author: Patrick Mair [cre, aut], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package sudokuAlt updated to version 0.1-5 with previous version 0.1-4 dated 2014-11-13

Title: Tools for Making, Displaying 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>

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Package zooaRch updated to version 1.1 with previous version 1.0 dated 2015-04-05

Title: Analytical Tools for Zooarchaeological Data
Description: The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.
Author: Erik Otarola-Castillo, Jesse Wolfhagen, Max D. Price
Maintainer: Erik Otarola-Castillo <eotarolacastillo@fas.harvard.edu>

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Package spTest updated to version 0.1.1 with previous version 0.1.0 dated 2015-05-09

Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>

Diff between spTest versions 0.1.0 dated 2015-05-09 and 0.1.1 dated 2015-07-24

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New package warbleR with initial version 1.0.1
Package: warbleR
Type: Package
Title: Streamline Bioacoustic Analysis
Version: 1.0.1
Date: 2015-07-22
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Description: Offers three overarching categories of functions to download recordings and metadata from Xeno Canto, manage sound files, and facilitate acoustic analysis in R.
License: GPL (>= 2)
Imports: rjson, pbapply, RCurl, fftw, utils, stats, grDevices, graphics
Depends: R (>= 2.10), maps, seewave (>= 2.0.1), tuneR
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-07-23 23:04:11 UTC; m
Repository: CRAN
Date/Publication: 2015-07-24 07:54:19

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Package seacarb updated to version 3.0.8 with previous version 3.0.6 dated 2015-02-03

Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph], Jean-Marie Epitalon [aut], Heloise Lavigne [aut], James Orr [ctb], Bernard Gentili [ctb], Andreas Hofmann [ctb], Aurélien Proye [ctb], Karline Soetaert [ctb], James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>

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Package rgbif updated to version 0.8.8 with previous version 0.8.6 dated 2015-07-03

Title: Interface to the Global 'Biodiversity' Information Facility 'API'
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, and getting counts of occurrence records.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Vijay Barve [aut], Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rEMM updated to version 1.0-11 with previous version 1.0-10 dated 2015-07-02

Title: Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Description: Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph], Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package recommenderlab updated to version 0.1-7 with previous version 0.1-6 dated 2015-07-02

Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package randomNames updated to version 0.1-0 with previous version 0.0-8 dated 2015-02-07

Title: Function for Generating Random Names and a Dataset
Description: Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner <dbetebenner@nciea.org>
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>

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Package powerSurvEpi updated to version 0.0.9 with previous version 0.0.6 dated 2012-03-31

Title: Power and Sample Size Calculation for Survival Analysis of Epidemiological Studies
Description: Functions to calculate power and sample size for testing main effect or interaction effect in the survival analysis of epidemiological studies (non-randomized studies), taking into account the correlation between the covariate of the interest and other covariates. Some calculations also take into account the competing risks and stratified analysis. This package also includes a set of functions to calculate power and sample size for testing main effect in the survival analysis of randomized clinical trials.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>, Jorge Chavarro <JCHAVARR@hsph.harvard.edu>, Ross Lazarus <ross.lazarus@channing.harvard.edu>, Bernard Rosner <stbar@channing.harvard.edu>, Jing Ma <jing.ma@channing.harvard.edu>.
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>

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Package npcp updated to version 0.1-6 with previous version 0.1-1 dated 2014-12-20

Title: Some Nonparametric Tests for Change-Point Detection in Possibly Multivariate Observations
Description: Provides nonparametric tests for assessing whether possibly serially dependent univariate or multivariate observations have the same c.d.f. or not. In addition to tests focusing directly on the c.d.f., the package contains tests designed to be particularly sensitive to changes in the underlying copula, Spearman's rho or certain quantities that can be estimated using one-sample U-statistics of order two such as the variance, Gini's mean difference or Kendall's tau. The latest addition is a nonparametric test for detecting changes in the distribution of independent block maxima.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>

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New package PharmacoGx with initial version 1.0.6
Package: PharmacoGx
Type: Package
Title: Large-Scale Analysis of Pharmacogenomic Data
Version: 1.0.6
Date: 2015-07-23
Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
License: Artistic-2.0
Suggests: xtable
Encoding: UTF-8
Imports: Biobase, piano, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices
Depends: R (>= 2.10)
URL: http://www.pmgenomics.ca/bhklab/software/pharmacogx
LazyData: yes
NeedsCompilation: no
Packaged: 2015-07-23 21:59:54 UTC; haibeb
Repository: CRAN
Date/Publication: 2015-07-24 07:53:45

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Package MazamaSpatialUtils updated to version 0.3.2 with previous version 0.3.1 dated 2015-07-10

Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized spatial polygons dataframes. Utility scripts use these datasets to return values such as country, state, timezone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre], Will Leahy [aut], Henry Nguyen [aut], Robin Winstanley [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>

Diff between MazamaSpatialUtils versions 0.3.1 dated 2015-07-10 and 0.3.2 dated 2015-07-24

 DESCRIPTION               |    6 +++---
 MD5                       |   10 +++++-----
 R/MazamaSpatialUtils.R    |    7 ++++++-
 R/getSpatialData.R        |   34 ++++++++++++++++++++++++++--------
 man/MazamaSpatialUtils.Rd |    7 ++++++-
 man/getSpatialData.Rd     |    9 ++++++---
 6 files changed, 52 insertions(+), 21 deletions(-)

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Package lessR updated to version 3.3.3 with previous version 3.3.1 dated 2015-04-28

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

Diff between lessR versions 3.3.1 dated 2015-04-28 and 3.3.3 dated 2015-07-24

 lessR-3.3.1/lessR/R/cor_resid.R            |only
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 lessR-3.3.3/lessR/DESCRIPTION              |   11 
 lessR-3.3.3/lessR/MD5                      |  117 ++---
 lessR-3.3.3/lessR/NAMESPACE                |   15 
 lessR-3.3.3/lessR/NEWS                     |   55 ++
 lessR-3.3.3/lessR/R/Correlation.R          |    4 
 lessR-3.3.3/lessR/R/Logit.R                |   13 
 lessR-3.3.3/lessR/R/Read.R                 |  111 +++--
 lessR-3.3.3/lessR/R/Regression.R           |   94 +++-
 lessR-3.3.3/lessR/R/Write.R                |    2 
 lessR-3.3.3/lessR/R/cfa.R                  |    2 
 lessR-3.3.3/lessR/R/corCFA.R               |  581 +++++++++++++++++-----------
 lessR-3.3.3/lessR/R/corEFA.R               |   95 +---
 lessR-3.3.3/lessR/R/corFA.zknitr.R         |  243 +++++++++--
 lessR-3.3.3/lessR/R/cor_mimm.R             |    6 
 lessR-3.3.3/lessR/R/cr.data.frame.R        |    5 
 lessR-3.3.3/lessR/R/details.R              |   47 +-
 lessR-3.3.3/lessR/R/dist.zknitr.R          |   33 +
 lessR-3.3.3/lessR/R/label.R                |   12 
 lessR-3.3.3/lessR/R/logit.z4Pred.R         |    2 
 lessR-3.3.3/lessR/R/reg.z1anvBasic.R       |    6 
 lessR-3.3.3/lessR/R/reg.z1bckBasic.R       |    7 
 lessR-3.3.3/lessR/R/reg.z1fitBasic.R       |    2 
 lessR-3.3.3/lessR/R/reg.z1modelBasic.R     |    4 
 lessR-3.3.3/lessR/R/reg.z2Relations.R      |   10 
 lessR-3.3.3/lessR/R/reg.z3dnResidual.R     |    4 
 lessR-3.3.3/lessR/R/reg.z3resfitResidual.R |    4 
 lessR-3.3.3/lessR/R/reg.z3txtResidual.R    |    8 
 lessR-3.3.3/lessR/R/reg.z4Pred.R           |    8 
 lessR-3.3.3/lessR/R/reg.z5Plot.R           |   10 
 lessR-3.3.3/lessR/R/reg.zknitr.R           |  595 +++++++++++++++++++----------
 lessR-3.3.3/lessR/R/scales.R               |    3 
 lessR-3.3.3/lessR/R/xAnd.R                 |only
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 lessR-3.3.3/lessR/R/zzz.R                  |  238 +++++++++--
 lessR-3.3.3/lessR/inst/CITATION            |    2 
 lessR-3.3.3/lessR/man/BarChart.Rd          |    9 
 lessR-3.3.3/lessR/man/BoxPlot.Rd           |    2 
 lessR-3.3.3/lessR/man/Density.Rd           |    2 
 lessR-3.3.3/lessR/man/Histogram.Rd         |    2 
 lessR-3.3.3/lessR/man/LineChart.Rd         |    2 
 lessR-3.3.3/lessR/man/Logit.Rd             |    4 
 lessR-3.3.3/lessR/man/Read.Rd              |   30 -
 lessR-3.3.3/lessR/man/Regression.Rd        |  100 ++--
 lessR-3.3.3/lessR/man/ScatterPlot.Rd       |   10 
 lessR-3.3.3/lessR/man/Subset.Rd            |    2 
 lessR-3.3.3/lessR/man/SummaryStats.Rd      |    2 
 lessR-3.3.3/lessR/man/Write.Rd             |    4 
 lessR-3.3.3/lessR/man/corCFA.Rd            |  153 +++++--
 lessR-3.3.3/lessR/man/corRead.Rd           |    4 
 lessR-3.3.3/lessR/man/label.Rd             |    4 
 lessR-3.3.3/lessR/man/ttest.Rd             |   28 -
 lessR-3.3.3/lessR/man/xAnd.Rd              |only
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 70 files changed, 1778 insertions(+), 929 deletions(-)

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Package ISOpureR updated to version 1.0.18 with previous version 1.0.8 dated 2015-01-08

Title: Deconvolution of Tumour Profiles
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros <Paul.Boutros@oicr.on.ca>

Diff between ISOpureR versions 1.0.8 dated 2015-01-08 and 1.0.18 dated 2015-07-24

 ISOpureR-1.0.18/ISOpureR/DESCRIPTION                                                                      |   10 
 ISOpureR-1.0.18/ISOpureR/MD5                                                                              |   64 
 ISOpureR-1.0.18/ISOpureR/NAMESPACE                                                                        |    6 
 ISOpureR-1.0.18/ISOpureR/NEWS                                                                             |   86 
 ISOpureR-1.0.18/ISOpureR/R/ISOpure.step1.CPE.R                                                            |only
 ISOpureR-1.0.18/ISOpureR/R/ISOpure.step2.PPE.R                                                            |only
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.new_model.R                                               |    2 
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.optmodel.R                                                |   23 
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_optimize.opt_kappa.R                                           |    2 
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_core.optmodel.R                                                |   23 
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.opt_kappa.R                                           |    2 
 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.theta.theta_loglikelihood.R                           |    2 
 ISOpureR-1.0.18/ISOpureR/build/vignette.rds                                                               |binary
 ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.Rnw                                                       |  871 ++++++++--
 ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.pdf                                                       |binary
 ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/alphapurities_full_dataset.txt                                 |only
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 ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/probeset_names.txt                                             |only
 ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step1_beer.R                                             |    3 
 ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step2_beer.R                                             |    3 
 ISOpureR-1.0.18/ISOpureR/man/ISOpure.step1.CPE.Rd                                                         |only
 ISOpureR-1.0.18/ISOpureR/man/ISOpure.step2.PPE.Rd                                                         |only
 ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_core.new_model.Rd                                            |    2 
 ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_optimize.opt_kappa.Rd                                        |    2 
 ISOpureR-1.0.18/ISOpureR/man/ISOpureS2.model_optimize.opt_kappa.Rd                                        |    2 
 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.cc_functions.R                               |    2 
 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R                         |    2 
 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.theta_functions.R                            |    2 
 ISOpureR-1.0.18/ISOpureR/vignettes/Figures                                                                |only
 ISOpureR-1.0.18/ISOpureR/vignettes/ISOpureRGuide.Rnw                                                      |  871 ++++++++--
 ISOpureR-1.0.8/ISOpureR/R/ISOpureS1.model_core.learnmodel.R                                               |only
 ISOpureR-1.0.8/ISOpureR/R/ISOpureS2.model_core.learnmodel.R                                               |only
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 ISOpureR-1.0.8/ISOpureR/man/ISOpureS1.model_core.learnmodel.Rd                                            |only
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 38 files changed, 1734 insertions(+), 246 deletions(-)

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Package influence.ME updated to version 0.9-6 with previous version 0.9-5 dated 2014-12-17

Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: Provides a collection of tools for detecting influential cases in generalized mixed effects models. It analyses models that were estimated using lme4. The basic rationale behind identifying influential data is that when iteratively single units are omitted from the data, models based on these data should not produce substantially different estimates. To standardize the assessment of how influential a (single group of) observation(s) is, several measures of influence are common practice, such as DFBETAS and Cook's Distance. In addition, we provide a measure of percentage change of the fixed point estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>

Diff between influence.ME versions 0.9-5 dated 2014-12-17 and 0.9-6 dated 2015-07-24

 DESCRIPTION                 |   10 
 MD5                         |   26 +-
 NAMESPACE                   |   44 ++--
 R/cooks.distance.extex.r    |    2 
 R/exclude.influence.R       |   21 +
 R/influence.R               |  483 ++++++++++++++++++++++----------------------
 man/cooks.distance.estex.Rd |    6 
 man/dfbetas.estex.Rd        |    6 
 man/exclude.influence.Rd    |    6 
 man/grouping.levels.Rd      |    2 
 man/influence.ME-package.Rd |    2 
 man/influence.mer.Rd        |   17 -
 man/pchange.Rd              |    4 
 man/plot.estex.Rd           |    2 
 14 files changed, 327 insertions(+), 304 deletions(-)

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Package in2extRemes updated to version 1.0-2 with previous version 1.0-1 dated 2014-01-28

Title: Into the extRemes Package
Description: Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>

Diff between in2extRemes versions 1.0-1 dated 2014-01-28 and 1.0-2 dated 2015-07-24

 DESCRIPTION |   12 ++++++------
 MD5         |    4 ++--
 NAMESPACE   |    5 +++++
 3 files changed, 13 insertions(+), 8 deletions(-)

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Package distillery updated to version 1.0-2 with previous version 1.0-1 dated 2013-06-26

Title: Method Functions for Confidence Intervals and to Distill Information from an Object
Description: Some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>

Diff between distillery versions 1.0-1 dated 2013-06-26 and 1.0-2 dated 2015-07-24

 DESCRIPTION |   13 +++++--------
 MD5         |    4 ++--
 NAMESPACE   |   10 ++++++++++
 3 files changed, 17 insertions(+), 10 deletions(-)

More information about distillery at CRAN
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