Thu, 08 Jan 2015

Package random updated to version 0.2.3 with previous version 0.2.2 dated 2013-12-11

Title: True Random Numbers using random.org
Description: The true random number service provided by the random.org website created by Mads Haahr samples atmospheric noise via radio tuned to an unused broadcasting frequency together with a skew correction algorithm due to John von Neumann. More background is available in the included vignette based on an essay by Mads Haahr. In its current form, the package offers functions to retrieve random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

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Package MCDA updated to version 0.0.8 with previous version 0.0.7 dated 2014-12-09

Title: Functions to support the Multicriteria Decision Aiding process
Description: MCDA, which stands for Multicriteria Decision Aiding, implements functions which can be useful to support the analyst in the decision aiding process involving multiple, conflicting criteria. These functions include, but are not limited to, data pre-processing tools, preference elicitation procedures, aggregation functions, as well as post-processing techniques and data visualisation functions.
Author: Patrick Meyer, Sébastien Bigaret.
Maintainer: Patrick Meyer

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Package MATA updated to version 0.2 with previous version 0.1 dated 2014-11-22

Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Provides a function for calculating the Model-Averaged Tail Area Wald (MATA-Wald) confidence interval, which is generated from single-model estimators and AIC model weights
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek

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Package circlize updated to version 0.2.1 with previous version 0.2.0 dated 2014-12-08

Title: Circular Visualization in R
Description: This package implements circular visualization (http://circos.ca/) in R. Due to the natural born feature of R to draw statistical graphics, this package can provide a more general and flexible way to visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu

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Package AICcmodavg updated to version 2.0-2 with previous version 2.0-1 dated 2014-10-17

Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). The package also features functions to conduct classic model averaging (multimodel inference) for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with Cox proportional hazards models and conditional logistic regression ('coxph' and 'coxme' classes), linear models ('lm' class), generalized linear models ('glm', 'vglm', 'hurdle', and 'zeroinfl' classes), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' and 'merMod' classes), multinomial and ordinal logistic regressions ('multinom'}, 'polr', 'clm', and 'clmm' classes), robust regression models ('rlm' class), beta regression models ('betareg' class), parametric survival models ('survreg' class), nonlinear models ('nls' and 'gnls' classes), and nonlinear mixed models ('nlme' and 'nlmer' classes). The package also supports various models of 'unmarkedFit' and 'maxLikeFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle .
Maintainer: Marc J. Mazerolle

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Package vows updated to version 0.3.1 with previous version 0.3 dated 2014-08-29

Title: Voxelwise semiparametrics
Description: Parametric and semiparametric inference for massively parallel models, i.e., a large number of models with common design matrix, as often occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, and Ruixin Tan
Maintainer: Philip Reiss

Diff between vows versions 0.3 dated 2014-08-29 and 0.3.1 dated 2015-01-08

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Package statar updated to version 0.1.3 with previous version 0.1.2 dated 2014-10-31

Title: Tools inspired by Stata to manipulate tabular data
Description: statar makes it easier to work with tabular datasets. The package includes a set of functions to clean and summarize variables, to join datasets using an SQL-syntax, to manipulate datasets with a panel structure (elapsed dates, lead/lag, rolling functions, fill in missing values based on previous dates, add rows for missing dates). The package also includes functions to emulate Stata and Julia string and expression interpolation. statar is based on the data.table package and is inspired by Stata.
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez

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Package brnn updated to version 0.5 with previous version 0.4 dated 2014-12-05

Title: brnn (Bayesian regularization for feed-forward neural networks)
Description: Bayesian regularization for feed-forward neural networks
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez

Diff between brnn versions 0.4 dated 2014-12-05 and 0.5 dated 2015-01-08

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Package XBRL updated to version 0.99.14 with previous version 0.99.13 dated 2014-11-18

Title: Extraction of Business Financial Information from XBRL Documents
Description: XBRL is a package suited to extract business financial information from an Extensible Business Reporting Language (XBRL) instance file and the associated collection of files that defines its Discoverable Taxonomy Set (DTS). These files are usually disseminated across different remote locations. XBRL documents employ many technologies defined by XML standards, such as XML Schema, Namespaces, XLink, and XPath, which make the extraction of information involved. The functions provided by this package address this complexity, returning data frames containing the enclosed information readily available to perform analyses. XBRL has been successfully tested in analyzing 10-K and 10-Q submissions from USA filing companies that are publicly available at the EDGAR system of the Securities and Exchange Commission (SEC). As published taxonomy files (such as "http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd") are immutable and are used by most filers, XBRL offers the option of downloading them only the first time they are referred, keeping a local cache copy that can be used from then on. This speeds-up the process, specially on slow connections. XBRL is not and does not aim to be (at least yet) a validating XBRL processor. XBRL is still a work in progress. As such, functions and produced data frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso

Diff between XBRL versions 0.99.13 dated 2014-11-18 and 0.99.14 dated 2015-01-08

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New package sra with initial version 0.1.1
Package: sra
Type: Package
Title: Selection Response Analysis
Version: 0.1.1
Date: 2015-01-08
Author: Arnaud Le Rouzic
Maintainer: Arnaud Le Rouzic
Imports: stats4
Description: This package (sra) provides a set of tools to analyse artificial-selection response datasets. The data typically feature for several generations the average value of a trait in a population, the variance of the trait, the population size and the average value of the parents that were chosen to breed. Sra implements two families of models aiming at describing the dynamics of the genetic architecture of the trait during the selection response. The first family relies on purely descriptive (phenomenological) models, based on an autoregressive framework. The second family provides different mechanistic models, accounting e.g. for inbreeding, mutations, genetic and environmental canalization, or epistasis. The parameters underlying the dynamics of the time series are estimated by maximum likelihood. The sra package thus provides (i) a wrapper for the R functions mle() and optim() aiming at fitting in a convenient way a predetermined set of models, and (ii) some functions to plot and analyze the output of the models.
License: GPL-2
Packaged: 2015-01-08 16:45:07 UTC; lerouzic
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-08 18:21:13

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New package noia with initial version 0.97.1
Package: noia
Type: Package
Title: Implementation of the Natural and Orthogonal InterAction (NOIA) model
Version: 0.97.1
Date: 2015-01-06
Author: Arnaud Le Rouzic (2007-2014), Arne B. Gjuvsland (2010), Olivier Ariste (2010)
Maintainer: Arnaud Le Rouzic
Depends: stats
LazyData: yes
Description: The NOIA model, as described extensively in Alvarez-Castro & Carlborg (2007), is a framework facilitating the estimation of genetic effects and genotype-to-phenotype maps. This package provides the basic tools to perform linear and multilinear regressions from real populations (provided the phenotype and the genotype of every individuals), estimating the genetic effects from different reference points, the genotypic values, and the decomposition of genetic variances in a multi-locus, 2 alleles system. This package is presented in Le Rouzic & Alvarez-Castro (2008).
License: GPL-2
Packaged: 2015-01-06 17:21:28 UTC; lerouzic
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-08 18:21:15

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Package ssym updated to version 1.5.2 with previous version 1.5.1 dated 2014-10-07

Title: Fitting Semi-parametric Log-symmetric Regression Models
Description: This package allows to to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, and asymmetric. In this setup, both median and skewness of the response variable distribution are explicitly modeled through semi-parametric functions, whose nonparametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas

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Package SimCorMultRes updated to version 1.3.0 with previous version 1.2 dated 2014-03-02

Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses by utilizing threshold approaches under a cumulative link model, a continuation ratio model or a baseline-category logit marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis

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Package ShrinkCovMat updated to version 1.1.0 with previous version 1.0.3 dated 2014-11-02

Title: Shrinkage Covariance Matrix Estimators
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis

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New package radir with initial version 1.0
Package: radir
Type: Package
Title: Inverse-Regression Estimation of Radioactive Doses
Version: 1.0
Date: 2014-10-03
Encoding: UTF-8
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler
Description: Radioactive doses estimation using individual chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm K. (2015). A new inverse regression model applied to radiation biodosimetry. Proceedings of the Royal Society A, 471
Depends: R (>= 3.1.1), hermite
Repository: CRAN
License: GPL (>= 2)
Packaged: 2015-01-08 12:50:59 UTC; dmorinya
NeedsCompilation: no
Date/Publication: 2015-01-08 17:02:05

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Package multicon updated to version 1.5 with previous version 1.3 dated 2014-10-30

Title: Multivariate Constructs
Description: Includes functions designed to examine relationships among multivariate constructs (e.g., personality). This includes functions for profile (within-person) analysis, dealing with large numbers of analyses, lens model analyses, and structural summary methods for data with circumplex structure. The package also includes functions for graphically comparing and displaying group means.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman

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Package curl updated to version 0.4 with previous version 0.3 dated 2014-12-01

Title: A Connection Interface to Libcurl
Description: The curl() function provides a drop-in replacement for base url() with better performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate and other libcurl goodies. This interface is implemented using the RConnection API in order to support incremental processing of both binary and text streams. If you are looking for a more-user-friendly http client, try the RCurl or httr packages instead.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between curl versions 0.3 dated 2014-12-01 and 0.4 dated 2015-01-08

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Package gstat updated to version 1.0-20 with previous version 1.0-19 dated 2014-04-02

Title: spatial and spatio-temporal geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre], Benedikt Graeler [aut]
Maintainer: Edzer Pebesma

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Package SemiParBIVProbit updated to version 3.2-13.1 with previous version 3.2-13 dated 2014-12-18

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-13 dated 2014-12-18 and 3.2-13.1 dated 2015-01-08

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New package qrLMM with initial version 1.0-9
Package: qrLMM
Type: Package
Title: Quantile Regression for Linear Mixed-Effects Models
Version: 1.0-9
Date: 2014-12-19
Author: Christian E. Galarza and Victor H. Lachos
Maintainer: Christian E. Galarza
Depends: nlme
Imports: matrixcalc, mvtnorm, ghyp, quantreg, psych, tcltk
Description: Quantile regression (QR) for Linear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides graphical summaries for assessing the algorithm convergence and fitting results.
License: GPL (>= 2)
Packaged: 2015-01-08 00:27:24 UTC; ra143711
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-08 12:24:39

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Package ISOpureR updated to version 1.0.8 with previous version 1.0.4 dated 2014-11-16

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

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Package io updated to version 0.2.2 with previous version 0.2.1 dated 2014-12-19

Title: A Unified Framework for Input-Output Operations in R
Description: One function to read files. One function to write files. One function to direct plots to screen or file. Automatic file format inference and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih

Diff between io versions 0.2.1 dated 2014-12-19 and 0.2.2 dated 2015-01-08

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New package interferenceCI with initial version 1.1
Package: interferenceCI
Type: Package
Title: Exact Confidence Intervals in the Presence of Interference
Version: 1.1
Date: 2015-1-7
Author: Joseph Rigdon
Maintainer: Joseph Rigdon
Depends: compiler, gtools
Description: Computes large sample confidence intervals of Liu and Hudgens (2014), exact confidence intervals of Tchetgen Tchetgen and VanderWeele (2012), and exact confidence intervals of Rigdon and Hudgens (2014) for treatment effects on a binary outcome in two-stage randomized experiments with interference.
License: GPL-3
Packaged: 2015-01-07 21:32:53 UTC; joe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-08 12:20:14

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Package ggRandomForests updated to version 1.1.3 with previous version 1.1.2 dated 2014-12-25

Title: Visually Exploring Random Forests
Description: Graphics for Random Forests using the randomForestSRC package for survival, regression and classification forests and ggplot2 package plotting.
Author: John Ehrlinger
Maintainer: John Ehrlinger

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Package FastHCS updated to version 0.0.4 with previous version 0.0.3 dated 2014-11-13

Title: FastHCS Robust Algortihm for Principal Component Analysis
Description: The FastHCS algorithm of Schmitt and Vakili (2014) for high-dimensional, robust PCA modelling and associated outlier detection and diagnostic tools.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili

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Package epiR updated to version 0.9-62 with previous version 0.9-61 dated 2014-12-17

Title: Tools for the Analysis of Epidemiological Data
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida and Simon Firestone
Maintainer: Mark Stevenson

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Package dplyr updated to version 0.4.0 with previous version 0.3.0.2 dated 2014-10-11

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre], Romain Francois [aut], RStudio [cph]
Maintainer: Hadley Wickham

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Package EMP updated to version 2.0.0 with previous version 1.0.2 dated 2014-08-24

Title: Expected Maximum Profit Classification Performance Measure
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014).
Author: Cristian Bravo, Seppe vanden Broucke and Thomas Verbraken
Maintainer: Cristian Bravo

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Package BANFF updated to version 0.2 with previous version 0.1 dated 2014-12-29

Title: Bayesian Network Feature Finder
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan

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Package acp updated to version 1.1 with previous version 1.0 dated 2014-07-23

Title: Autoregressive Conditional Poisson
Description: Time series analysis of count data
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios

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Package sp updated to version 1.0-17 with previous version 1.0-16 dated 2014-11-09

Title: classes and methods for spatial data
Description: A package that provides classes and methods for spatial data. The classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb]
Maintainer: Edzer Pebesma

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