Sat, 31 Jan 2015

Package llama updated to version 0.8 with previous version 0.7.2 dated 2014-09-20

Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb]
Maintainer: Lars Kotthoff

Diff between llama versions 0.7.2 dated 2014-09-20 and 0.8 dated 2015-01-31

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 llama-0.8/llama/R/zzz.R                                                |    5 
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More information about llama at CRAN
Permanent link

Package fclust updated to version 1.1 with previous version 1.0.1 dated 2014-03-26

Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results
Author: Paolo Giordani, Maria Brigida Ferraro
Maintainer: Paolo Giordani

Diff between fclust versions 1.0.1 dated 2014-03-26 and 1.1 dated 2015-01-31

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Package simPH updated to version 1.2.6.1 with previous version 1.2.4 dated 2014-12-07

Title: Tools for Simulating and Plotting Quantities of Interest Estimated From Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

Diff between simPH versions 1.2.4 dated 2014-12-07 and 1.2.6.1 dated 2015-01-31

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Package flexCWM updated to version 1.4 with previous version 1.3 dated 2014-12-16

Title: Flexible Cluster-Weighted Modeling
Description: Allows for maximum likelihood fitting of cluster-weighted models, a class of mixtures of regression models with random covariates.
Author: Mazza A., Punzo A., Ingrassia S.
Maintainer: Angelo Mazza

Diff between flexCWM versions 1.3 dated 2014-12-16 and 1.4 dated 2015-01-31

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Package dendextend updated to version 0.18.3 with previous version 0.17.5 dated 2014-09-22

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

Diff between dendextend versions 0.17.5 dated 2014-09-22 and 0.18.3 dated 2015-01-31

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More information about dendextend at CRAN
Permanent link

Package cluster updated to version 2.0.1 with previous version 2.0.0 dated 2015-01-29

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster analysis methods. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990).
Author: Martin Maechler [aut, cre], Peter Rousseeuw [aut] (Fortran original), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)), Matthias Studer [ctb], Pierre Roudier [ctb]
Maintainer: Martin Maechler

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More information about cluster at CRAN
Permanent link

Package lmomco updated to version 2.1.3 with previous version 2.1.1 dated 2014-06-02

Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
Description: Extensive functions for the theory of L-moments (LMs) in addition to probability-weighted moments (PWMs), and parameter (p) estimation for numerous familiar and not-so-familiar distributions. Estimation of LMs for the same distributions is provided as are L-moment ratio diagrams. Estimation of LMs for right-tail and left-tail censoring by known or unknown threshold and also by indicator variable is available. Asymmetric trimmed LMs (TL-moments, TLMs) are supported as are numerical integrations to dynamically compute trajectories of select TLM ratios for TL-moment ratio diagram construction. LMs of residual (resid.) and reversed (rev.) resid. life are implemented along with 13 operators on quantile functions that are useful in reliability, lifetime, and survival analysis. Exact analytical bootstrap estimates of order statistics, LMs, and variances-covariances of LMs are provided. The Harri-Coble Tau34-squared Test for Normality is available. Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail censoring (RC) encompasses: Asymmetric (Asy.) Exponential (Exp.) Power [L], Asy. Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen.) Exp. Poisson [L], Gen. Extreme Value [L], Gen. Lambda [L,TL], Gen. Logistic [L), Gen. Normal [L], Gen. Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev. Gumbel [L+RC], Rice/Rician (L), Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L]. LMs have multivariate analogs; the sample L-comoments (LCMs) are implemented and might have considerable application with copulas because LCMs measure asymmetric association and higher comoments or comovements of variables.
Author: William Asquith
Maintainer: William Asquith

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Package LMERConvenienceFunctions updated to version 2.10 with previous version 2.5 dated 2013-12-14

Title: Model Selection and Post-hoc Analysis for (G)LMER Models
Description: The main function of the package is to perform backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. The data to run examples is contained in package LCF_data.
Author: Antoine Tremblay, Dalhousie University, and Johannes Ransijn, University of Copenhagen
Maintainer: "Antoine Tremblay, Dalhousie University"

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Package d3Network updated to version 0.5.2.1 with previous version 0.5.1 dated 2014-07-13

Title: Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R
Description: This packages is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames. !!! NOTE: Active development has moved to the networkD3 package. !!!
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

Diff between d3Network versions 0.5.1 dated 2014-07-13 and 0.5.2.1 dated 2015-01-31

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Package DataCombine updated to version 0.2.8.3 with previous version 0.2.7.1 dated 2014-12-08

Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

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Package BayesCR updated to version 2.0 with previous version 1.0 dated 2013-11-02

Title: Bayesian Analysis of Censored Regression Models Under Scale Mixture of Skew Normal Distributions
Description: Propose a parametric fit for censored linear regression models based on SMSN distributions, from a Bayesian perspective. Also, generates SMSN random variables.
Author: Aldo M. Garay , Monique B. Massuia Victor H. Lachos
Maintainer: Aldo M. Garay

Diff between BayesCR versions 1.0 dated 2013-11-02 and 2.0 dated 2015-01-31

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Package opencpu updated to version 1.4.6 with previous version 1.4.5 dated 2014-11-08

Title: A System for Embedded Scientific Computing and Reproducible Research with R
Description: The OpenCPU system exposes an HTTP API for embedded scientific computing with R. This provides scalable foundations for integrating R based analysis and visualization modules into pipelines, web applications or big data infrastructures. The OpenCPU server can run either as a single-user development server within the interactive R session, or as a high performance multi-user cloud server that builds on Linux, Nginx and rApache. The current R package forms the core of the system. When loaded in R, it automatically initiates the single-user server and displays the web address in the console. Visit the OpenCPU website for detailed information and documentation on the API.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

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Package wgaim updated to version 1.4-5 with previous version 1.4-3 dated 2014-09-03

Title: Whole Genome Average Interval Mapping for QTL Detection using Mixed Models
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor , Simon Diffey , Ari Verbyla and Brian Cullis .
Maintainer: Julian Taylor

Diff between wgaim versions 1.4-3 dated 2014-09-03 and 1.4-5 dated 2015-01-31

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Package mixlm updated to version 1.0.8.1 with previous version 1.0.8 dated 2015-01-21

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

Diff between mixlm versions 1.0.8 dated 2015-01-21 and 1.0.8.1 dated 2015-01-31

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Fri, 30 Jan 2015

Package stylo updated to version 0.5.9 with previous version 0.5.8-2 dated 2014-10-19

Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder

Diff between stylo versions 0.5.8-2 dated 2014-10-19 and 0.5.9 dated 2015-01-30

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Package GSIF updated to version 0.4-4 with previous version 0.4-3 dated 2014-12-09

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [ctb], Gerard Heuvelink [ctb], Brendan Malone [ctb]
Maintainer: Tomislav Hengl

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Package copBasic updated to version 1.7.1 with previous version 1.7.0 dated 2015-01-03

Title: General Copula Theory and Many Utility Functions
Description: Extensive functions for copula computations and related mathematical operations are given that are oriented around the oft cited and fundamental copula theory described by Nelsen (2006), Joe (2015), and other selected works. The lower, upper, product, and select other copulas are implemented. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, co-copula, and numerical copula density. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses; functions for copula simulation thus are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) random variates of composited copulas. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma, tail dependency, and tail order. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. The Kullback-Leibler divergence and Vuong's Procedure to support inference are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith

Diff between copBasic versions 1.7.0 dated 2015-01-03 and 1.7.1 dated 2015-01-30

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More information about copBasic at CRAN
Permanent link

Package shinyFiles updated to version 0.5.0 with previous version 0.4.0 dated 2014-09-23

Title: A server-side file system viewer for shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location.
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen

Diff between shinyFiles versions 0.4.0 dated 2014-09-23 and 0.5.0 dated 2015-01-30

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Package mvoutlier updated to version 2.0.6 with previous version 2.0.5 dated 2014-06-23

Title: Multivariate outlier detection based on robust methods
Description: various methods for multivariate outlier detection.
Author: Peter Filzmoser and Moritz Gschwandtner
Maintainer: Peter Filzmoser

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Package SmarterPoland updated to version 1.5 with previous version 1.2 dated 2013-03-18

Title: Tools for Accessing Various Datasets Developed by the Foundation SmarterPoland.pl
Description: Tools for accessing and processing datasets presented on the blog SmarterPoland.pl. Among all: functions for downloading data from eurostat database, coordinates from Google Maps and data from GUS (Central Statistical Office of Poland).
Author: Przemyslaw Biecek (Foundation SmarterPoland.pl)
Maintainer: Przemyslaw Biecek

Diff between SmarterPoland versions 1.2 dated 2013-03-18 and 1.5 dated 2015-01-30

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Package rockchalk updated to version 1.8.91 with previous version 1.8.86 dated 2014-08-13

Title: Regression Estimation and Presentation
Description: A collection of functions for ease of presentation and interpretation of regression analysis. These functions are used to produce the statistics lectures in http://pj.freefaculty.org/guides. There are functions to explore the effect (or lack thereof) from "mean centering," "residual centering", and standardization. The vignette "rockchalk" offers a fairly comprehensive overview. The vignette "Rstyle" has advice about coding in R. See the outreg function for a convenient way to generate regression models for reports. For nice, easy to use pictures, see plotSlopes, plotCurves, plotPlane. The package title "rockchalk" refers to our school motto, "Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson

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Package P2C2M updated to version 0.6 with previous version 0.5 dated 2014-10-24

Title: Posterior Predictive Checks of Coalescent Models
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST or *BEAST. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, the installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is required.
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl

Diff between P2C2M versions 0.5 dated 2014-10-24 and 0.6 dated 2015-01-30

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Permanent link

Package DiagrammeR updated to version 0.4 with previous version 0.1 dated 2015-01-09

Title: Create Diagrams and Flowcharts Using R
Description: With the DiagrammeR package, you can create diagrams and flowcharts using R. Markdown-like text is used to describe a diagram and, by doing this in R, we can also add some R code into the mix and integrate these diagrams in the R console, through R Markdown, and in shiny apps.
Author: knsv [aut, cph] (mermaid.js library in htmlwidgets/lib, http://github.com/knsv/mermaid/), Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib, http://github.com/cpettitt/dagre-d3), mdaines [aut, cph] (viz.js library in htmlwidgets/lib, http://github.com/mdaines/viz.js/), Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone

Diff between DiagrammeR versions 0.1 dated 2015-01-09 and 0.4 dated 2015-01-30

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Package dataRetrieval updated to version 2.1.1 with previous version 2.1.0 dated 2014-12-17

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from the National Water Information Services (NWIS) tools found here: http://waterservices.usgs.gov/ Both EPA and USGS water quality data are obtained from the Water Quality Portal found here: http://www.waterqualitydata.us/portal.jsp
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut]
Maintainer: Laura DeCicco

Diff between dataRetrieval versions 2.1.0 dated 2014-12-17 and 2.1.1 dated 2015-01-30

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More information about dataRetrieval at CRAN
Permanent link

Package climdex.pcic updated to version 1.1-5 with previous version 1.1-4 dated 2014-11-19

Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of extreme climate indices.
Author: David Bronaugh for the Pacific Climate Impacts Consortium
Maintainer: James Hiebert

Diff between climdex.pcic versions 1.1-4 dated 2014-11-19 and 1.1-5 dated 2015-01-30

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Package circlize updated to version 0.2.2 with previous version 0.2.1 dated 2015-01-08

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 brewdata updated to version 0.4 with previous version 0.3 dated 2015-01-28

Title: Extracting Usable Data from the Grad Cafe Results Search
Description: Retrieves and parses graduate admissions survey data from the Grad Cafe website (http://thegradcafe.com).
Author: Nathan Welch
Maintainer: Nathan Welch

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Thu, 29 Jan 2015

Package portfolio updated to version 0.4-7 with previous version 0.4-6 dated 2013-07-09

Title: Analysing equity portfolios
Description: Classes for analysing and implementing equity portfolios.
Author: Jeff Enos and David Kane , with contributions from Daniel Gerlanc and Kyle Campbell
Maintainer: Daniel Gerlanc

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Package AGSDest updated to version 2.2 with previous version 2.1 dated 2013-11-06

Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence intervals based on the stage-wise ordering in group sequential designs and adaptive group sequential designs. For adaptive group sequential designs the confidence intervals are based on the conditional rejection probability principle. Currently the procedures do not support the use of futility boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner

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Package StatMatch updated to version 1.2.3 with previous version 1.2.2 dated 2014-06-19

Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio

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Package biotools updated to version 2.0 with previous version 1.2 dated 2014-05-25

Title: Tools for Biometry and Applied Statistics in Agricultural Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva

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Package GetoptLong updated to version 0.0.9 with previous version 0.0.8 dated 2014-11-05

Title: Parsing Command-line Arguments and Variable Interpolation
Description: Parsing command-line arguments by Perl module Getopt::Long. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu

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Package cluster updated to version 2.0.0 with previous version 1.15.3 dated 2014-09-04

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis Methods. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre], Peter Rousseeuw [aut] (Fortran original), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)), Matthias Studer [ctb], Pierre Roudier [ctb]
Maintainer: Martin Maechler

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Package Luminescence updated to version 0.4.1 with previous version 0.4.0 dated 2014-12-18

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

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Package teigen updated to version 2.0.8 with previous version 2.0.7 dated 2014-08-19

Title: Model-Based Clustering and Classification with the Multivariate t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews

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Wed, 28 Jan 2015

Package packrat updated to version 0.4.3 with previous version 0.4.2-1 dated 2014-12-16

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: A tool for managing the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey

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Package metaMA updated to version 3.1.2 with previous version 3.1.1 dated 2015-01-26

Title: Meta-analysis for MicroArrays
Description: Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
Author: Guillemette Marot
Maintainer: Guillemette Marot

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Package marmap updated to version 0.9.2 with previous version 0.9.1 dated 2014-12-16

Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante

Diff between marmap versions 0.9.1 dated 2014-12-16 and 0.9.2 dated 2015-01-28

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Package GlobalOptions updated to version 0.0.6 with previous version 0.0.5 dated 2014-12-24

Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GlobalOptions versions 0.0.5 dated 2014-12-24 and 0.0.6 dated 2015-01-28

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Package visualFields updated to version 0.4.2 with previous version 0.4 dated 2014-03-03

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch
Maintainer: Ivan Marin-Franch

Diff between visualFields versions 0.4 dated 2014-03-03 and 0.4.2 dated 2015-01-28

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Package SMNCensReg updated to version 3.0 with previous version 2.4 dated 2014-07-17

Title: Fitting Univariate Censored Regression Model Under the Family of Scale Mixture of Normal Distributions
Description: Fit univariate right, left or interval censored regression model under the scale mixture of normal distributions
Author: Aldo M. Garay , Monique Bettio Massuia and Victor Lachos
Maintainer: Aldo M. Garay

Diff between SMNCensReg versions 2.4 dated 2014-07-17 and 3.0 dated 2015-01-28

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Package plotKML updated to version 0.5-0 with previous version 0.4-8 dated 2014-12-09

Title: Visualization of Spatial and Spatio-temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl

Diff between plotKML versions 0.4-8 dated 2014-12-09 and 0.5-0 dated 2015-01-28

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Package MarkowitzR updated to version 0.1502 with previous version 0.1402 dated 2014-02-12

Title: Statistical Significance of the Markowitz Portfolio
Description: a collection of tools for analyzing significance of Markowitz portfolios.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav

Diff between MarkowitzR versions 0.1402 dated 2014-02-12 and 0.1502 dated 2015-01-28

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Package LaF updated to version 0.6.2 with previous version 0.6.1 dated 2014-04-21

Title: Fast access to large ASCII files
Description: Methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (csv) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.
Author: Jan van der Laan
Maintainer: Jan van der Laan

Diff between LaF versions 0.6.1 dated 2014-04-21 and 0.6.2 dated 2015-01-28

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Package KFKSDS updated to version 1.6 with previous version 1.5 dated 2014-07-27

Title: Kalman Filter, Smoother and Disturbance Smoother
Description: Naive implementation of the Kalman filter, smoother and disturbance smoother for state space models.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between KFKSDS versions 1.5 dated 2014-07-27 and 1.6 dated 2015-01-28

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Package CpGassoc updated to version 2.50 with previous version 2.11 dated 2014-01-10

Title: Association Between Methylation and a Phenotype of Interest
Description: Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield

Diff between CpGassoc versions 2.11 dated 2014-01-10 and 2.50 dated 2015-01-28

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Package stochvol updated to version 1.0.0 with previous version 0.9-1 dated 2014-12-27

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner

Diff between stochvol versions 0.9-1 dated 2014-12-27 and 1.0.0 dated 2015-01-28

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Package kedd updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-18

Title: Kernel Estimator and Bandwidth Selection for Density and its Derivatives
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum

Diff between kedd versions 1.0.1 dated 2014-08-18 and 1.0.2 dated 2015-01-28

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Package VineCopula updated to version 1.4 with previous version 1.3 dated 2014-04-22

Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package CDVine are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler
Maintainer: Tobias Erhardt

Diff between VineCopula versions 1.3 dated 2014-04-22 and 1.4 dated 2015-01-28

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Package RInside updated to version 0.2.12 with previous version 0.2.11 dated 2014-02-12

Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications The RInside packages makes it easier to have 'R inside' your C++ application by providing a C++ wrapper class providing the R interpreter. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the eight subdirectories of the examples/ directory of the installed package: standard, mpi (for parallel computing) qt (showing how to embed RInside inside a Qt GUI application), wt (showing how to build a 'web-application' using the Wt toolkit), armadillo (for RInside use with RcppArmadillo) and eigen (for RInside use with RcppEigen). The example use GNUmakefile(s) with GNU extensions, so a GNU make is required (and will use the GNUmakefile automatically). Doxygen-generated documentation of the C++ classes is available at the RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel

Diff between RInside versions 0.2.11 dated 2014-02-12 and 0.2.12 dated 2015-01-28

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Package MVN updated to version 3.8 with previous version 3.7 dated 2014-11-16

Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz

Diff between MVN versions 3.7 dated 2014-11-16 and 3.8 dated 2015-01-28

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Package SLHD updated to version 2.1-1 with previous version 1.2-1 dated 2013-05-14

Title: Maximin-Distance (Sliced) Latin Hypercube Designs
Description: Generate the optimal Latin Hypercube Designs (LHDs) for computer experiments with quantitative factors and the optimal Sliced Latin Hypercube Designs (SLHDs) for computer experiments with both quantitative and qualitative factors. Details of the algorithm can be found in Ba, S., Brenneman, W. A. and Myers, W. R. (2015), "Optimal Sliced Latin Hypercube Designs," Technometrics. Important function in this package is "maximinSLHD".
Author: Shan Ba
Maintainer: Shan Ba

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Package rvalues updated to version 0.3 with previous version 0.2 dated 2014-07-24

Title: R-values for Ranking in High-Dimensional Settings
Description: A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
Author: Nicholas Henderson and Michael Newton
Maintainer: Nicholas Henderson

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Package RandomFields updated to version 3.0.60 with previous version 3.0.59 dated 2015-01-27

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging; maximum likelihood estimation
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], 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

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Package numbers updated to version 0.5-2 with previous version 0.4-5 dated 2014-01-08

Title: Number-theoretic Functions
Description: Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers

Diff between numbers versions 0.4-5 dated 2014-01-08 and 0.5-2 dated 2015-01-28

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Package NeuralNetTools updated to version 1.0.1 with previous version 1.0.0 dated 2014-12-16

Title: Visualization and Analysis Tools for Neural Networks
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck

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Package fanplot updated to version 3.4.0 with previous version 3.3 dated 2014-08-01

Title: Visualisation of Sequential Probability Distributions Using Fan Charts
Description: Visualise sequential distributions using a range of plotting styles. Sequential distribution data can be input as either simulations or values corresponding to percentiles over time. Plots are added to existing graphic devices using the fan function. Users can choose from four different styles, including fan chart type plots, where a set of coloured polygon, with shadings corresponding to the percentile values are layered to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel"

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Tue, 27 Jan 2015

Package plotROC updated to version 1.3 with previous version 1.2 dated 2014-11-13

Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
Author: Michael C Sachs
Maintainer: Michael C Sachs

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Package tufterhandout updated to version 1.2.1 with previous version 1.2 dated 2014-11-12

Title: Tufte-style html document format for rmarkdown
Description: Custom template and output formats for use with rmarkdown. Produce Edward Tufte-style handouts in html formats with full support for rmarkdown features
Author: Michael C Sachs
Maintainer: Michael C Sachs

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Package tsoutliers updated to version 0.6 with previous version 0.5 dated 2015-01-25

Title: Detection of Outliers in Time Series
Description: Detection of outliers in time series following the Chen and Liu (1993) procedure. Innovative outliers, additive outliers, level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

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Package rplexos updated to version 0.12 with previous version 0.11 dated 2014-12-16

Title: Read and Analyze PLEXOS Solutions from R
Description: Efficiently read and analyze PLEXOS solutions by converting them into SQLite databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

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Package MCMC.qpcr updated to version 1.1.5 with previous version 1.1.3 dated 2014-04-13

Title: Bayesian analysis of qRT-PCR data
Description: This package implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. Tutorial: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz

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Package Ecfun updated to version 0.1-4 with previous version 0.1-3 dated 2014-11-27

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves

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Package CLME updated to version 2.0-2 with previous version 2.0-1 dated 2014-12-05

Title: Constrained Inference for Linear Mixed Effects Models
Description: Constrained inference for linear mixed effects models using residual bootstrap methodology
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema

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Package unmarked updated to version 0.10-6 with previous version 0.10-5 dated 2015-01-23

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler

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Package MaxPro updated to version 3.1-2 with previous version 3.1-1 dated 2015-01-27

Title: Maximum Projection Designs
Description: Generate a maximum projection (MaxPro) design, a MaxPro Latin hypercube design or improve an initial design based on the MaxPro criterion. Details of the MaxPro criterion can be found in: Joseph, V. R., Gul, E., and Ba, S. (2015) "Maximum Projection Designs for Computer Experiments", Biometrika.
Author: Shan Ba and V. Roshan Joseph
Maintainer: Shan Ba

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Package TraMineRextras updated to version 0.2.3 with previous version 0.2.2 dated 2013-10-29

Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph], Matthias Studer [aut], Reto Buergin [aut], Alexis Gabadinho [ctb], Nicolas Muller [ctb], Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard

Diff between TraMineRextras versions 0.2.2 dated 2013-10-29 and 0.2.3 dated 2015-01-27

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Package TraMineR updated to version 1.8-9 with previous version 1.8-8 dated 2014-01-14

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: This is a toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph], Nicolas Muller [aut], Reto Buergin [aut], Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard

Diff between TraMineR versions 1.8-8 dated 2014-01-14 and 1.8-9 dated 2015-01-27

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Package sequenza updated to version 2.1.1 with previous version 2.1.0 dated 2014-10-08

Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero

Diff between sequenza versions 2.1.0 dated 2014-10-08 and 2.1.1 dated 2015-01-27

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Package SCVA updated to version 1.1.1 with previous version 1.1 dated 2014-09-02

Title: Single-Case Visual Analysis
Description: A package to make graphical representations of single case data and to transform graphical displays back to raw data. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between SCVA versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27

 DESCRIPTION         |    8 ++++----
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Package SCRT updated to version 1.1.1 with previous version 1.1 dated 2014-09-02

Title: Single-Case Randomization Tests
Description: A package for designing single-case phase, alternation and multiple-baseline experiments, as well as for conducting randomization tests on data gathered by means of such designs.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between SCRT versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27

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Package SCMA updated to version 1.1.1 with previous version 1.1 dated 2014-01-13

Title: Single-Case Meta-Analysis
Description: An R package for single-case meta-analysis.
Author: Isis Bulte
Maintainer: Bart Michiels

Diff between SCMA versions 1.1 dated 2014-01-13 and 1.1.1 dated 2015-01-27

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Package RcmdrPlugin.SCDA updated to version 1.1 with previous version 1.0 dated 2014-03-19

Title: Rcmdr Plugin for Designing and Analyzing Single-case Experiments
Description: Provides a GUI for the SCVA, SCRT and SCMA packages. The package is written as an Rcmdr plugin.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between RcmdrPlugin.SCDA versions 1.0 dated 2014-03-19 and 1.1 dated 2015-01-27

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Package qrLMM updated to version 1.1 with previous version 1.0-9 dated 2015-01-08

Title: Quantile Regression for Linear Mixed-Effects Models
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.
Author: Christian E. Galarza and Victor H. Lachos
Maintainer: Christian E. Galarza

Diff between qrLMM versions 1.0-9 dated 2015-01-08 and 1.1 dated 2015-01-27

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Package openair updated to version 1.1-3 with previous version 1.1-0 dated 2015-01-05

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw

Diff between openair versions 1.1-0 dated 2015-01-05 and 1.1-3 dated 2015-01-27

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Package msarc updated to version 1.4.5 with previous version 1.4.3 dated 2014-12-04

Title: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments
Description: The output of an affinity-purification mass spectrometry experiment is typically a list of proteins that were observed in the experiment, identified by UniProt identifiers (http://www.uniprot.org/). This package takes as input a list of UniProt identifiers, and the associated Mascot scores from the experiment (which indicate the likelihood that the protein has been correctly identified), clusters them by gene ontology category (http://geneontology.org/), then draws diagrams showing the results in hierarchical clusters by category, with lines for individual proteins representing the associated Mascot score. The results are in general not publication-ready, but will rather require editing via a graphics editor that can interpret SVG (scalable vector graphics) format. As an alternative representation, the package will also generate tag clouds based on the Mascot scores.
Author: Gord Brown, Hisham Mohammed
Maintainer: Gord Brown

Diff between msarc versions 1.4.3 dated 2014-12-04 and 1.4.5 dated 2015-01-27

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Package lawstat updated to version 2.5 with previous version 2.4.1 dated 2013-12-16

Title: Tools for Biostatistics, Public Policy, and Law
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, measures of relative variability etc, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.
Author: (in alphabetical order) Joseph L. Gastwirth ; Yulia R. Gel ; W. L. Wallace Hui ; Weiwen Miao ; Kimihiro Noguchi
Maintainer: Vyacheslav Lyubchich

Diff between lawstat versions 2.4.1 dated 2013-12-16 and 2.5 dated 2015-01-27

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Package HMR updated to version 0.4.1 with previous version 0.3.2 dated 2014-12-12

Title: Flux Estimation with Static Chamber Data
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen
Maintainer: Asger R. Pedersen

Diff between HMR versions 0.3.2 dated 2014-12-12 and 0.4.1 dated 2015-01-27

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Package decompr updated to version 2.0 with previous version 1.3.2 dated 2014-12-10

Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Description: Two Global Value Chains decompositions are implemented. Firstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross exports into 16 value added components. Secondly, the Leontief decomposition (default) derives the value added origin of exports by country and industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre], Fei Wang [aut], Victor Kummritz [aut]
Maintainer: Bastiaan Quast

Diff between decompr versions 1.3.2 dated 2014-12-10 and 2.0 dated 2015-01-27

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Package PHENIX updated to version 1.1 with previous version 1.0 dated 2014-10-24

Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), a bootstrapping method to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares

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Package FeedbackTS updated to version 1.3.1 with previous version 1.3 dated 2015-01-05

Title: Analysis of Feedback in Time Series
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand

Diff between FeedbackTS versions 1.3 dated 2015-01-05 and 1.3.1 dated 2015-01-27

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Package raster updated to version 2.3-24 with previous version 2.3-12 dated 2014-10-18

Title: Geographic data analysis and modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans

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More information about raster at CRAN
Permanent link

Package RandomFields updated to version 3.0.59 with previous version 3.0.55 dated 2015-01-14

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging; maximum likelihood estimation
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], 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

Diff between RandomFields versions 3.0.55 dated 2015-01-14 and 3.0.59 dated 2015-01-27

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 134 files changed, 8627 insertions(+), 6337 deletions(-)

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Package PerMallows updated to version 1.8 with previous version 1.7 dated 2014-09-15

Title: Permutations and Mallows Distributions
Description: Includes functions to work with the Mallows, Generalized Mallows and Weighted Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances and the random generation of permutations.
Author: Ekhine Irurozki
Maintainer: Ekhine Irurozki

Diff between PerMallows versions 1.7 dated 2014-09-15 and 1.8 dated 2015-01-27

 DESCRIPTION                            |   10 
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 src/Ulam.h                             |   51 +---
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 src/Wrapper.cpp                        |    9 
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 66 files changed, 943 insertions(+), 1135 deletions(-)

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Package CORElearn updated to version 0.9.45 with previous version 0.9.44 dated 2014-12-24

Title: Classification, Regression and Feature Evaluation
Description: The package is a port of stand-alone C++ software to R. It contains several machine learning model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leafs, random forests, kNN, naive Bayes, and locally weighted regression. It is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM. Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class. Several algorithms support parallel multithreaded execution via OpenMP. The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja"

Diff between CORElearn versions 0.9.44 dated 2014-12-24 and 0.9.45 dated 2015-01-27

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 NAMESPACE                |   37 +-
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 71 files changed, 1303 insertions(+), 1070 deletions(-)

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Package spBayes updated to version 0.3-9 with previous version 0.3-8 dated 2013-11-15

Title: Univariate and Multivariate Spatial-temporal Modeling
Description: Fits univariate and multivariate spatio-temporal models with Markov chain Monte Carlo (MCMC).
Author: Andrew O. Finley , Sudipto Banerjee
Maintainer: Andrew O. Finley

Diff between spBayes versions 0.3-8 dated 2013-11-15 and 0.3-9 dated 2015-01-27

 DESCRIPTION          |   10 +++++-----
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Package smacof updated to version 1.6-2 with previous version 1.5-0 dated 2014-06-23

Title: Multidimensional Scaling in R: SMACOF.
Description: This package provides the following approaches of multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): Simple smacof (basic MDS) on symmetric dissimilarity matrices, smacof for rectangular matrices (unfolding models), smacof with constraints on the configuration, three-way smacof for individual differences (including constraints for idioscal, indscal, and identity), and spherical smacof (primal and dual algorithm). The MDS type can be ratio, interval, ordinal manner (including primary, secondary, and tertiary approaches for tie handling), and msplines. Jackknife and permutation tests are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Ingwer Borg [ctb], Patrick J. F. Groenen [aut]
Maintainer: Patrick Mair

Diff between smacof versions 1.5-0 dated 2014-06-23 and 1.6-2 dated 2015-01-27

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Package reldist updated to version 1.6-4 with previous version 1.6-3 dated 2014-08-20

Title: Relative Distribution Methods
Description: R functions for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the Social Sciences" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789
Author: Mark S. Handcock
Maintainer: Mark S. Handcock

Diff between reldist versions 1.6-3 dated 2014-08-20 and 1.6-4 dated 2015-01-27

 DESCRIPTION          |   10 +++++-----
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Package munfold updated to version 0.3-3 with previous version 0.3-1 dated 2013-01-05

Title: Metric Unfolding
Description: This package provides Schoeneman's algorithm for metric multidimensional unfolding and Procrustes rotation of unfolding results.
Author: Martin Elff
Maintainer: Martin Elff

Diff between munfold versions 0.3-1 dated 2013-01-05 and 0.3-3 dated 2015-01-27

 DESCRIPTION     |   18 ++++++++++--------
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 R/Unfold.R      |    4 ++--
 R/schoenemann.R |    5 ++---
 inst            |only
 6 files changed, 34 insertions(+), 32 deletions(-)

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Package icd9 updated to version 1.0 with previous version 0.5 dated 2014-07-21

Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, and perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9-CM (clinical modification) codes. ICD-9 codes appear numeric but leading and trailing zeroes, and both decimal and non-decimal "short" format codes exist. The package enables a work flow from raw lists of ICD-9 codes from hospital billing databases to comorbidities. ICD-9 to comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey

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Package gridSVG updated to version 1.4-3 with previous version 1.4-2 dated 2014-12-16

Title: Export grid Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG format. Additional functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut], Simon Potter [aut]
Maintainer: Paul Murrell

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Package geoCount updated to version 1.150120 with previous version 1.131209 dated 2013-12-09

Title: Analysis and Modeling for Geostatistical Count Data
Description: This package provides a variety of functions to analyze and model geostatistical count data with generalized linear spatial models, including 1) simulate and visualize the data; 2) posterior sampling with robust MCMC algorithms (in serial or parallel way); 3) perform prediction for unsampled locations; 4) conduct Bayesian model checking procedure to evaluate the goodness of fitting; 5) conduct transformed residual checking procedure. In the package, seamlessly embedded C++ programs and parallel computing techniques are implemented to speed up the computing processes.
Author: Liang Jing
Maintainer: Liang Jing

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Mon, 26 Jan 2015

Package stsm updated to version 1.7 with previous version 1.4 dated 2014-07-27

Title: Structural Time Series Models
Description: Fit the basic structural time series model by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

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Package micromap updated to version 1.9.1 with previous version 1.9 dated 2014-05-27

Title: Linked Micromap Plots
Description: This group of functions simplifies the creation of linked micromap plots.
Author: Quinn Payton [aut], Tony Olsen [aut], Marc Weber [ctb], Michael McManus [ctb], Tom Kincaid [cre, ctb]
Maintainer: Tom Kincaid

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Package dygraphs updated to version 0.4.1 with previous version 0.3.3 dated 2014-12-23

Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the dygraphs JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib, http://dygraphs.com/), JJ Allaire [aut, cre] (R interface), RStudio [cph]
Maintainer: JJ Allaire

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Package simPop updated to version 0.2.9 with previous version 0.2.6 dated 2014-11-18

Title: Simulation of Synthetic Populations for Survey Data Considering Auxiliary Information
Description: Simulate populations for surveys based on auxiliary data including model-based methods, calibration and combinatorial optimization tools. Developed with support of the International Household Survey Network, DFID Trust Fund TF011722
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ

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 NEWS                       |   61 ++++++----
 R/0classes.R               |    2 
 R/addKnownMargins.R        |    4 
 R/addWeights.r             |    2 
 R/calibPop.R               |   18 +-
 R/calibSample.R            |    8 -
 R/calibVars.R              |    2 
 R/ipu.r                    |    2 
 R/printFunctions.R         |    2 
 R/simCategorical.R         |   16 +-
 R/simComponents.R          |   12 -
 R/simContinuous.R          |   14 +-
 R/simEUSILC.R              |   36 ++---
 R/simInitSpatial.R         |   16 +-
 R/simRelation.R            |   18 +-
 R/simStructure.R           |    2 
 R/spBwplot.R               |    4 
 R/spCdfplot.R              |    4 
 R/spTable.R                |    4 
 R/synthPop.R               |   14 +-
 R/utils.R                  |    6 
 inst/CITATION              |   19 ++-
 man/addKnownMargins.Rd     |    6 
 man/addWeights-methods.Rd  |    8 -
 man/calibPop.Rd            |   14 +-
 man/calibSample-methods.Rd |    6 
 man/dataObj-class.Rd       |    2 
 man/manageSynthPopObj.Rd   |   22 +--
 man/simCategorical.Rd      |   14 +-
 man/simComponents.Rd       |   26 ++--
 man/simContinuous.Rd       |   12 -
 man/simEUSILC.Rd           |    2 
 man/simInitSpatial.Rd      |   14 +-
 man/simRelation.Rd         |    8 -
 man/simStructure.Rd        |    2 
 man/spBwplot.Rd            |    6 
 man/spCdfplot.Rd           |    6 
 man/spTable.Rd             |    2 
 man/synthPop-methods.Rd    |   36 ++---
 man/synthPopObj-class.Rd   |   14 +-
 src/calibPop.cpp           |   24 +--
 src/calibVars.cpp          |    2 
 src/ipu.cpp                |    2 
 tests/test_sprague.R       |  274 +++++++++++++++++++++++++++++++++++++++++++++
 47 files changed, 591 insertions(+), 281 deletions(-)

More information about simPop at CRAN
Permanent link

Package rmarkdown updated to version 0.5.1 with previous version 0.4.2 dated 2014-12-22

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats including HTML, MS Word, PDF, and Beamer.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire

Diff between rmarkdown versions 0.4.2 dated 2014-12-22 and 0.5.1 dated 2015-01-26

 DESCRIPTION                                             |   72 +++++++++-
 MD5                                                     |  113 ++++++++--------
 NAMESPACE                                               |    2 
 NEWS                                                    |   10 +
 R/beamer_presentation.R                                 |    3 
 R/draft.R                                               |    4 
 R/html_document.R                                       |    8 -
 R/html_document_base.R                                  |    3 
 R/html_fragment.R                                       |    3 
 R/html_vignette.R                                       |    2 
 R/ioslides_presentation.R                               |    5 
 R/md_document.R                                         |    3 
 R/output_format.R                                       |    4 
 R/pandoc.R                                              |    8 -
 R/pdf_document.R                                        |    6 
 R/relative_to.R                                         |    7 
 R/render.R                                              |   21 +-
 R/shiny.R                                               |    6 
 R/slidy_presentation.R                                  |    3 
 R/tufte_handout.R                                       |    4 
 R/util.R                                                |    4 
 inst/NOTICE                                             |    5 
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 inst/rmd/latex/default.tex                              |    6 
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 man/beamer_presentation.Rd                              |   11 -
 man/default_output_format.Rd                            |    3 
 man/draft.Rd                                            |    3 
 man/html_document.Rd                                    |    7 
 man/html_document_base.Rd                               |    3 
 man/html_fragment.Rd                                    |    9 -
 man/html_vignette.Rd                                    |    8 -
 man/includes.Rd                                         |    3 
 man/ioslides_presentation.Rd                            |    8 -
 man/knitr_options.Rd                                    |    3 
 man/knitr_options_html.Rd                               |    7 
 man/knitr_options_pdf.Rd                                |    7 
 man/md_document.Rd                                      |    7 
 man/metadata.Rd                                         |    3 
 man/output_format.Rd                                    |    3 
 man/pandoc_args.Rd                                      |    3 
 man/pandoc_available.Rd                                 |    3 
 man/pandoc_convert.Rd                                   |    3 
 man/pandoc_options.Rd                                   |    3 
 man/pandoc_path_arg.Rd                                  |    3 
 man/pandoc_self_contained_html.Rd                       |    3 
 man/pandoc_template.Rd                                  |    3 
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 man/relative_to.Rd                                      |    3 
 man/render.Rd                                           |    4 
 man/render_delayed.Rd                                   |    3 
 man/render_supporting_files.Rd                          |    3 
 man/rmarkdown_format.Rd                                 |    3 
 man/run.Rd                                              |    3 
 man/slidy_presentation.Rd                               |    7 
 man/tufte_handout.Rd                                    |    7 
 man/word_document.Rd                                    |    3 
 58 files changed, 318 insertions(+), 151 deletions(-)

More information about rmarkdown at CRAN
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Package metaRNASeq updated to version 1.0.2 with previous version 0.4 dated 2014-03-14

Title: Meta-analysis of RNA-seq data
Description: Implementation of two p-value combination techniques (inverse normal and Fisher methods). A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments.
Author: Guillemette Marot, Florence Jaffrezic, Andrea Rau
Maintainer: Guillemette Marot

Diff between metaRNASeq versions 0.4 dated 2014-03-14 and 1.0.2 dated 2015-01-26

 DESCRIPTION               |   17 ++---
 MD5                       |   42 ++++++------
 NAMESPACE                 |    9 +-
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 build/vignette.rds        |binary
 data/dispFuncs.rda        |binary
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 inst/NEWS                 |    4 +
 inst/doc/metaRNASeq.R     |   47 ++++++++++++-
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 man/param.Rd              |   68 ++++++++++----------
 man/rawpval.Rd            |   52 +++++++--------
 man/sim.function.Rd       |  138 ++++++++++++++++++++--------------------
 vignettes/metaRNASeq.Rnw  |   74 ++++++++++++++++-----
 vignettes/metaRNASeq.bib  |   56 ++++++++++------
 23 files changed, 562 insertions(+), 417 deletions(-)

More information about metaRNASeq at CRAN
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Package metaMA updated to version 3.1.1 with previous version 2.1 dated 2011-08-29

Title: Meta-analysis for MicroArrays
Description: Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
Author: Guillemette Marot
Maintainer: Guillemette Marot

Diff between metaMA versions 2.1 dated 2011-08-29 and 3.1.1 dated 2015-01-26

 DESCRIPTION                   |   18 ++--
 MD5                           |   38 +++++----
 NAMESPACE                     |only
 R/EScombination.R             |  168 ++++++++++++++++++++---------------------
 R/EScombination.paired.R      |  114 ++++++++++++++--------------
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 man/metaMA-package.Rd         |   80 ++++++++++---------
 man/pvalcombination.Rd        |   96 +++++++++++------------
 man/pvalcombination.paired.Rd |   96 +++++++++++------------
 man/row.ttest.stat.Rd         |    2 
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 20 files changed, 633 insertions(+), 613 deletions(-)

More information about metaMA at CRAN
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Package BayesVarSel updated to version 1.6.1 with previous version 1.5.1 dated 2014-03-25

Title: Bayes Factors, Model Choice And Variable Selection In Linear Models
Description: Conceived to calculate Bayes factors in linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in the package is placed on the prior distributions and BayesVarSel allows using a wide range of them: Jeffreys-Zellner-Siow (Jeffreys, 1961; Zellner and Siow, 1980,1984) Zellner (1986); Fernandez et al. (2001), Liang et al. (2008) and Bayarri et al. (2012). The interaction with the package is through a friendly interface that syntactically mimics the well-known lm command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the true -data generating- model. Additionally, BayesVarSel incorporates abilities to handle problems with a large number of potential explanatory variables through parallel and heuristic versions (Garcia-Donato and Martinez-Beneito 2013) of the main commands.
Author: Gonzalo Garcia-Donato and Anabel Forte
Maintainer: Anabel Forte

Diff between BayesVarSel versions 1.5.1 dated 2014-03-25 and 1.6.1 dated 2015-01-26

 BayesVarSel-1.5.1/BayesVarSel/R/predict.Bvs.R            |only
 BayesVarSel-1.5.1/BayesVarSel/R/print.Bvs.predict.R      |only
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 BayesVarSel-1.6.1/BayesVarSel/DESCRIPTION                |   17 
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 BayesVarSel-1.6.1/BayesVarSel/NAMESPACE                  |    5 
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 BayesVarSel-1.6.1/BayesVarSel/R/Bvs.R                    |  436 +
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 BayesVarSel-1.6.1/BayesVarSel/R/PBvs.R                   |  399 +
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 BayesVarSel-1.6.1/BayesVarSel/man/Bvs.Rd                 |   52 
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 BayesVarSel-1.6.1/BayesVarSel/man/PBvs.Rd                |   28 
 BayesVarSel-1.6.1/BayesVarSel/man/bayesvarsel-package.rd |   17 
 BayesVarSel-1.6.1/BayesVarSel/man/plotbvs.rd             |    2 
 BayesVarSel-1.6.1/BayesVarSel/src/Gibbsauxiliaryfuncs.c  |    2 
 BayesVarSel-1.6.1/BayesVarSel/src/allBF.c                |   23 
 BayesVarSel-1.6.1/BayesVarSel/src/allBF.h                |    1 
 BayesVarSel-1.6.1/BayesVarSel/src/auxiliaryfuncs.c       |   91 
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 BayesVarSel-1.6.1/BayesVarSel/src/main.c                 | 4479 +++++++++++----
 BayesVarSel-1.6.1/BayesVarSel/src/mainGibbs.c            | 3925 +++++++++++--
 BayesVarSel-1.6.1/BayesVarSel/src/mainSingle.c           |   15 
 BayesVarSel-1.6.1/BayesVarSel/src/priorprob.c            |    2 
 29 files changed, 8088 insertions(+), 1960 deletions(-)

More information about BayesVarSel at CRAN
Permanent link


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