Thu, 26 Nov 2015

Package OneArmPhaseTwoStudy updated to version 0.1.4 with previous version 0.1.3 dated 2015-07-01

Title: Planing, Monitoring and Evaluating Oncological Phase 2 Studies
Description: Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with this package a good starting point is to take a closer look at the functions getSolutions() and getSolutionsSub1().
Author: Marius Wirths
Maintainer: Marius Wirths <wirths@imbi.uni-heidelberg.de>

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New package forestmodel with initial version 0.3.3
Package: forestmodel
Type: Package
Title: Forest Plots from Regression Models
Version: 0.3.3
Date: 2015-11-25
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>
Description: Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
License: GPL-2
LazyData: TRUE
Depends: R (>= 3.2.0), ggplot2 (>= 1.0.1)
Imports: dplyr (>= 0.4.2), broom (>= 0.3.7), lazyeval (>= 0.1.10)
Suggests: survival, metafor
NeedsCompilation: no
Packaged: 2015-11-26 14:10:02 UTC; Nick
Repository: CRAN
Date/Publication: 2015-11-26 17:03:11

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Package equateIRT updated to version 1.2-1 with previous version 1.2 dated 2014-11-14

Title: Direct, Chain and Average Equating Coefficients with Standard Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

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Package treeclim updated to version 1.0.13 with previous version 1.0.11 dated 2015-02-10

Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions, seasonal correlations and evaluation of reconstruction skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl], Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>

Diff between treeclim versions 1.0.11 dated 2015-02-10 and 1.0.13 dated 2015-11-26

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Package RJSDMX updated to version 1.5 with previous version 1.4 dated 2015-07-22

Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers that disseminate data by means of SDMX web services. SDMX (Statistical Data and Metadata eXchange) is a standard that has been developed with the aim of simplifying the exchange of statistical information. More about the SDMX standard and the SDMX Web Services can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>

Diff between RJSDMX versions 1.4 dated 2015-07-22 and 1.5 dated 2015-11-26

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Package markovchain updated to version 0.4.3 with previous version 0.4.2 dated 2015-08-24

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

Diff between markovchain versions 0.4.2 dated 2015-08-24 and 0.4.3 dated 2015-11-26

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New package NEpiC with initial version 1.0
Package: NEpiC
Type: Package
Title: Network Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals
Version: 1.0
Date: 2015-11-26
Author: Peifeng Ruan
Depends: igraph
Maintainer: Peifeng Ruan <pruan12@fudan.edu.cn>
Description: Package for a Network assisted algorithm for Epigenetic studies using mean and variance Combined signals: NEpiC. NEpiC combines both signals in mean and variance differences in methylation level between case and control groups searching for differentially methylated sub-networks (modules) using the protein-protein interaction network.
License: GPL-2
Packaged: 2015-11-26 09:35:56 UTC; win7
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-11-26 14:15:18

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New package GroupTest with initial version 1.0.1
Package: GroupTest
Type: Package
Title: Multiple Testing Procedure for Grouped Hypotheses
Version: 1.0.1
Date: 2015-11-20
Author: Zhigen Zhao
Maintainer: Zhigen Zhao <zhaozhg@temple.edu>
Description: Contains functions for a two-stage multiple testing procedure for grouped hypothesis, aiming at controlling both the total posterior false discovery rate and within-group false discovery rate.
License: GPL-3
Packaged: 2015-11-26 12:38:17 UTC; zhaozhg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-11-26 14:25:49

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Package flacco updated to version 1.1 with previous version 1.0 dated 2015-10-28

Title: Feature-Based Landscape Analysis of Continuous and Constraint Optimization Problems
Description: Contains tools and features, which can be used for an exploratory landscape analysis of continuous optimization problems. Those are able to quantify rather complex properties, such as the global structure, separability, etc., of continuous optimization problems.
Author: Pascal Kerschke [aut, cre], Jan Dagefoerde [aut]
Maintainer: Pascal Kerschke <kerschke@uni-muenster.de>

Diff between flacco versions 1.0 dated 2015-10-28 and 1.1 dated 2015-11-26

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Package SocialMediaLab updated to version 0.19.0 with previous version 0.18.0 dated 2015-11-15

Title: Tools for Collecting Social Media Data and Generating Networks for Analysis
Description: A suite of tools for collecting and constructing networks from social media data. Provides easy-to-use functions for collecting data across popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating different types of networks for analysis.
Author: Timothy Graham & Robert Ackland
Maintainer: Timothy Graham <timothy.graham3@uq.net.au>

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Package rvertnet updated to version 0.4.0 with previous version 0.3.4 dated 2015-09-16

Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives. Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rchallenge updated to version 1.1.1 with previous version 1.1 dated 2015-05-17

Title: A Simple Data Science Challenge System
Description: A simple data science challenge system using R Markdown and Dropbox <https://www.dropbox.com/>. It requires no network configuration, does not depend on external platforms like e.g. Kaggle <https://www.kaggle.com/> and can be easily installed on a personal computer.
Author: Adrien Todeschini [aut, cre], Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>

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Package Power2Stage updated to version 0.4-3 with previous version 0.4-2 dated 2015-07-17

Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies
Description: Functions to obtain the operational characteristics of bioequivalence studies with 2-stage designs via simulations - Contains a function to calculate power and sample-size distribution of 2-stage bioequivalence (BE) studies with a 2x2 crossover design according to Potvin et al. / Montague et al. modified to include a futility Nmax and modified to do the sample size estimation step with PE and mse of stage 1. - Contains further a function with the modifications according to Karalis & Macheras which use both point estimate (PE) and mse from stage 1 also for the power monitoring steps. - The third function power.2stage.fC() calculates power and sample-size distribution of 2-stage BE studies with a futility criterion for the PE or CI of T/R from stage 1. - The fourth function power.2stage.GS() calculates power of non-adaptive group sequential (2-stage) BE studies. - The fifth function power.2stage.p() calculates power and sample size distribution of 2-stage BE studies with 2 parallel groups. This function has a sibling power.2stage.pAF(), which performs exactly as described in A.Fuglsang 2014 - Another function power.2stage.ssr() allows the power calculation for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre], Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

Diff between Power2Stage versions 0.4-2 dated 2015-07-17 and 0.4-3 dated 2015-11-26

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 19 files changed, 260 insertions(+), 158 deletions(-)

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Package nleqslv updated to version 2.9.1 with previous version 2.9 dated 2015-09-06

Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>

Diff between nleqslv versions 2.9 dated 2015-09-06 and 2.9.1 dated 2015-11-26

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Package mlr updated to version 2.6 with previous version 2.5 dated 2015-11-20

Title: Machine Learning in R
Description: Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Richter [aut], Jakob Bossek [aut], Leonard Judt [aut], Tobias Kuehn [aut], Erich Studerus [aut], Lars Kotthoff [aut], Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>

Diff between mlr versions 2.5 dated 2015-11-20 and 2.6 dated 2015-11-26

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Package gets updated to version 0.3 with previous version 0.2 dated 2014-12-22

Title: General-to-Specific (GETS) Modelling and Indicator Saturation Methods
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Felix Pretis, James Reade, Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>

Diff between gets versions 0.2 dated 2014-12-22 and 0.3 dated 2015-11-26

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New package clogitboost with initial version 1.0
Package: clogitboost
Type: Package
Title: Boosting Conditional Logit Model
Version: 1.0
Date: 2015-11-09
Authors@R: c(person("Haolun","Shi", email = "shl2003@connect.hku.hk", role = c("aut", "cre")), person("Guosheng","Yin", email = "gyin@hku.hk", role = "aut") )
Author: Haolun Shi [aut, cre], Guosheng Yin [aut]
Maintainer: Haolun Shi <shl2003@connect.hku.hk>
Description: A set of functions to fit a boosting conditional logit model.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp
LazyData: True
NeedsCompilation: yes
Packaged: 2015-11-26 03:00:26 UTC; ra3
Repository: CRAN
Date/Publication: 2015-11-26 08:33:10

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Package circlize updated to version 0.3.3 with previous version 0.3.2 dated 2015-10-21

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

Diff between circlize versions 0.3.2 dated 2015-10-21 and 0.3.3 dated 2015-11-26

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 62 files changed, 543 insertions(+), 169 deletions(-)

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Package brotli updated to version 0.4 with previous version 0.3 dated 2015-10-06

Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the LZ77 algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but offers more dense compression.
Author: Jeroen Ooms [aut, cre], Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between brotli versions 0.3 dated 2015-10-06 and 0.4 dated 2015-11-26

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