Numerical Analysis and Scientific Computing Commons^™

Rcmdrplugin.Temis, A Graphical Integrated Text Mining Solution In R, Milan Bouchet-Valat, Gilles Bastin

The R Journal

We present the package RcmdrPlugin.temis, a graphical user interface for user-friendly text mining in R. Built as a plug-in to the R Commander provided by the Rcmdr package, it brings together several existing packages and provides new features streamlining the process of importing, managing and analyzing a corpus, in addition to saving results and plots to a report file. Beyond common-file formats, automated import of corpora from the Dow Jones Factiva content provider and Twitter is supported. Featured analyses include vocabulary and dissimilarity tables, terms frequencies, terms specific of levels of a variable, term co-occurrences, time series, correspondence analysis …

Conference Report: R/Finance 2013, Joshua Ulrich

The R Journal

The fifth annual R/Finance conference for applied finance using R was held in Chicago, IL, USAonFriday May17andSaturday May 18, 2013.

The conference provided a venue to discuss how R can be used for portfolio management, time series analysis, advanced risk analysis, high-performance computing, market microstructure, and econometrics. As in prior years, the conference had 300 attendees from several countries (including several European countries, South Africa, Australia, and Russia). The program included seminars, keynotes, full-length talks, and lightning talks. The conference also provided exceptional networking opportunities.

The R Journal (June 2013) 5(1): Complete Issue, The R Foundation

The R Journal

Editorial, Hadley Wickham

Contributed Research Articles

RTextTools: A Supervised Learning Package for Text Classification, Timothy P. Jurka, Loren Collingwood, Amber E. Boydstun, Emiliano Grossman, and Wouter van Atteveldt

Generalized Simulated Annealing for Global Optimization: The GenSA Package, Yang Xiang, Sylvain Gubian, Brian Suomela, and Julia Hoeng

Multiple Factor Analysis for Contingency Tables in the FactoMineR Package, Belchin Kostov, Mónica Bécue-Bertaut, and François Husson

Hypothesis Tests for Multivariate Linear Models Using the car Package, John Fox, Michael Friendly, and Sanford Weisberg

osmar: OpenStreetMap and R, Manuel J. A. Eugster and Thomas Schlesinger

ftsa: An R Package for Analyzing Functional Time Series, …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

The R Journal (December 2012) 4(2): Complete Issue, The R Foundation

The R Journal

Contributing Articles

What's in a Name? Paul Murrell

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

Debugging grid Graphics, Paul Murrell and Velvet Ly

frailtyHL: A Package for Fitting Frailty Models with H-likelihood, Il Do Ha, Maengseok Noh, and Youngjo Lee

influence.ME: Tools for Detecting Influential Data in Mixed Effects Models, Rense Nieuwenhuis, Manfred te Grotenhuis and Ben Pelzer

The crs Package: Nonparametric Regression Splines for Continuous and Categorical Predictors, Zhenghua Nie and Jeffrey S. Racine

Rfit: Rank-based Estimation for Linear Models, John D. Kloke and Joseph W. McKean

Graphical Markov Models with Mixed Graphs in …

The Crs Package: Nonparametric Regression Splines For Continuous And Categorical Predictors, Zhenghua Nie, Jeffery S. Racine

The R Journal

A new package crs is introduced for computing nonparametric regression (and quantile) splines in the presence of both continuous and categorical predictors. B-splines are employed in the regression model for the continuous predictors and kernel weighting is employed for the categorical predictors. We also de velop a simple R interface to NOMAD, which is a mixed integer optimization solver used to compute optimal regression spline solutions.

Influence.Me: Tools For Detecting Influential Data In Mixed Effects Models, Rense Nieuwenhuis, Manfred Te Grotenhuis, Ben Pelzer

The R Journal

influence.ME provides tools for detecting influential data in mixed effects models. The application of these models has become common practice, but the development of diagnostic tools has lagged behind. influence.ME calculates standardized measures of influential data for the point estimates of generalized mixed effects models, such as DFBETAS, Cook’s distance, as well as percentile change and a test for changing levels of significance. influence.ME calculates these measures of influence while ac counting for the nesting structure of the data. The package and measures of influential data are introduced, a practical example is given, and strategies for dealing with influential data …

Graphical Markov Models With Mixed Graphs In R, Kayvan Sadeghi, Giovanni M. Marchetti

The R Journal

In this paper we provide a short tuto rial illustrating the new functions in the package ggm that deal with ancestral, summary and ribbonless graphs. These are mixed graphs (containing three types of edges) that are important because they capture the modified independence structure after marginalisation over, and conditioning on, nodes of directed acyclic graphs. We provide functions to verify whether a mixed graph implies that A is independent of B given C for any disjoint sets of nodes and to generate maximal graphs inducing the same independence structure of non-maximal graphs. Finally, we provide functions to decide on the …

What's In A Name?, Paul Murrell

The R Journal

Any shape that is drawn using the grid graphics package can have a name associated with it. If a name is provided, it is possible to access, query, and modify the shape after it has been drawn. These facilities allow for very detailed customisations of plots and also for very general transformations of plots that are drawn by packages based on grid.

Frailtyhl: A Package For Fitting Frailty Models With H-Likelihood, Il Do Ha, Maengseok Noh, Youngjo Lee

The R Journal

We present the frailtyHL package for fitting semi-parametric frailty models using h likelihood. This package allows lognormal or gamma frailties for random-effect distribution, and it fits shared or multilevel frailty models for correlated survival data. Functions are provided to format and summarize the frailtyHL results. The estimates of fixed effects and frailty parameters and their standard errors are calculated. We illustrate the use of our package with three well known data sets and compare our results with various alternative R-procedures.

Rfit: Rank-Based Estimation For Linear Models, John D. Kloke, Joseph W. Mckeen

The R Journal

In the nineteen seventies, Jureĉková and Jaeckel proposed rank estimation for linear models. Since that time, several authors have developed inference and diagnostic methods for these estimators. These rank-based estimators and their associated inference are highly efficient and are robust to outliers in response space. The methods include estimation of standard errors, tests of general linear hypotheses, confidence intervals, diagnostic procedures including studentized residuals, and measures of influential cases. We have developed an R package, Rfit, for computing of these robust procedures. In this paper we highlight the main features of the pack age. The package uses standard linear …

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

The R Journal

The R graphics engine has new support for drawing complex paths via the functions polypath() and grid.path(). This article explains what is meant by a complex path and demonstrates the usefulness of complex paths in drawing non-trivial shapes, logos, customised data symbols, and maps.

Debugging Grid Graphics, Paul Murrell, Velvet Ly

The R Journal

A graphical scene that has been produced using the grid graphics package consists of grobs (graphical objects) and viewports. This article describes functions that allow the exploration and inspection of the grobs and viewports in a grid scene, including several functions that are available in a new package called gridDe bug. The ability to explore the grobs and view ports in a grid scene is useful for adding more drawing to a scene that was produced using grid and for understanding and debugging the grid code that produced a scene.

The State Of Naming Conventions In R, Rasmus Bååth

The R Journal

Most programming language communities have naming conventions that are generally agreed upon, that is, a set of rules that governs how functions and variables are named. This is not the case with R, and a review of unofficial style guides and naming convention us age on CRAN shows that a number of different naming conventions are currently in use. Some naming conventions are, however, more popular than others and as a newcomer to the R community or as a developer of a new package this could be useful to consider when choosing what naming convention to adopt.

Retrieval Of Sub-Pixel-Based Fire Intensity And Its Application For Characterizing Smoke Injection Heights And Fire Weather In North America, David Peterson

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

For over two decades, satellite sensors have provided the locations of global fire activity with ever-increasing accuracy. However, the ability to measure fire intensity, know as fire radiative power (FRP), and its potential relationships to meteorology and smoke plume injection heights, are currently limited by the pixel resolution. This dissertation describes the development of a new, sub-pixel-based FRP calculation (FRP_f) for fire pixels detected by the MODerate Resolution Imaging Spectroradiometer (MODIS) fire detection algorithm (Collection 5), which is subsequently applied to several large wildfire events in North America. The methodology inherits an earlier bi-spectral algorithm for retrieving sub-pixel …

The R Journal (June 2012) 4(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Analysing Seasonal Data, Adrian G. Barnett, Peter Baker, and Annette J. Dobson

MARSS: Multivariate Autoregressive State-space Models for Analyzing Time-series Data, Elizabeth E. Holmes, Eric J. Ward, and Kellie Wills

openair: Data Analysis Tools for the Air Quality Community, Karl Ropkins and David C. Carslaw

Foreign Library Interface, Daniel Adler

Vdgraph: A Package for Creating Variance Dispersion Graphs, John Lawson

xgrid and R: Parallel Distributed Processing Using Heterogeneous Groups of Apple Computers, Sarah C. Anoke, Yuting Zhao, Rafael Jaeger, and Nicholas J. Horton

maxent: An R Package for Low-memory Multinomial Logistic Regression with Support for Semi-automated Text …

Who Did What? The Roles Of R Package Authors And How To Refer To Them, Kurt Hornik, Duncan Murdoch, Achim Zeileis

The R Journal

Computational infrastructure for rep resenting persons and citations has been avail able in R for several years, but has been restructured through enhanced classes "person" and "bibentry" in recent versions of R. The new features include support for the specification of the roles of package authors (e.g. maintainer, author, contributor, translator, etc.) and more flexible formatting/printing tools among various other improvements. Here, we introduce the new classes and their methods and indicate how this functionality is employed in the management of R packages. Specifically, we show how the authors of R packages can be specified along with their roles in …

Xgrid And R: Parallel Distributed Processing Using Heterogeneous Groups Of Apple Computers, Sarah C. Anoke, Yuting Zhao, Rafael Jaeger, Nicholas J. Horton

The R Journal

The Apple Xgrid system provides access to groups (or grids) of computers that can be used to facilitate parallel processing. We describe the xgrid package which facilitates access to this system to undertake independent simulations or other long-running jobs that can be divided into replicate runs within R. Detailed examples are provided to demonstrate the interface, along with results from a simulation study of the performance gains using a variety of grids. Use of the grid for “embarassingly parallel” independent jobs has the potential for major speedups in time to completion. Appendices provide guidance on setting up the workflow, utilizing …

Openair: Data Analysis Tools For The Air Quality Community, Karl Ropkins, David C. Carslaw

The R Journal

The openair package contains data analysis tools for the air quality community. This paper provides an overview of data importers, main functions, and selected utilities and workhorse functions within the package and the function output class, as of package version 0.4-14. It is intended as an explanation of the rationale for the package and a technical description for those wishing to work more inter actively with the main functions or develop additional functions to support ‘higher level’ use of openair and R.

Maxent: An R Package For Low-Memory Multinomial Logistic Regression With Support For Semi-Automated Text Classification, Timothy P. Jurka

The R Journal

maxent is a package with tools for data classification using multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm text mining pack age.

Marss: Multivariate Autoregressive State-Space Models For Analyzing Time-Series Data, Elizabeth E. Holmes, Eric J. Ward, Kellie Wills

The R Journal

MARSS is a package for fitting multivariate autoregressive state-space models to time-series data. The MARSS package implements state-space models in a maximum likelihood framework. The core functionality of MARSSis based on likelihood maximization using the Kalman filter/smoother, combined with an EM algorithm. To make comparisons with other packages available, parameter estimation is also permitted via direct search routines avail able in ’optim’. The MARSS package allows data to contain missing values and allows a wide variety of model structures and constraints to be specified (such as fixed or shared parameters). In addition to model-fitting, the package provides bootstrap routines for …

Vdgraph: A Package For Creating Variance Dispersion Graphs, John Lawson

The R Journal

This article introduces the package Vdgraph that is used form a king variance dispersion graphs of response surface designs.The package includes functions that make the variance dispersion graph of one design or compare variance dispersion graphs of two designs, which are stored in data frames or matrices.The package also contains several minimum run response surface designs (stored as matrices) that are not available in other R packages.

Analysing Seasonal Data, Adrian G. Barnett, Peter Baker, Annette J. Dobson

The R Journal

Many common diseases, such as the flu and cardiovascular disease, increase markedly in winter and dip in summer. These seasonal patterns have been part of life for millennia and were first noted in ancient Greece by both Hippocrates and Herodotus. Recent interest has focused on climate change, and the concern that seasons will become more extreme with harsher winter and summer weather. We describe a set of R functions designed to model seasonal pat terns in disease. We illustrate some simple descriptive and graphical methods, a more complex method that is able to model non-stationary patterns, and the case-crossover to …

Foreign Library Interface, Daniel Adler

The R Journal

We present an improved Foreign Function Interface (FFI) for R to call arbitary native functions without the need for C wrapper code. Further we discuss a dynamic linkage framework for binding standard C libraries to R across platforms using a universal type information format. The package rdyncall comprises the framework and an initial repository of cross platform bindings for standard libraries such as (legacy and modern) OpenGL, the family of SDL libraries and Expat. The package enables system level programming using the R language; sample applications are given in the article. We out line the underlying automation tool-chain that extracts …

Sumo: An Authenticating Web Application With An Embedded R Session, Timothy T. Bergsma, Michael S. Smith

The R Journal

Sumo is a web application intended as a template for developers. It is distributed as a Java ‘war’ file that deploys automatically when placed in a Servlet container’s ‘webapps’ directory. If a user supplies proper credentials, Sumocreates a session-specific Secure Shell connection to the host and a user-specific R session over that connection. Developers may write dynamic server pages that make use of the persistent R session and user-specific file space. The supplied example plots a data set conditional on preferences indicated by the user; it also displays some static text. A companion server page al lows the user to …

The R Journal (December 2011) 3(2): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Creating and Deploying an Application with (R)Excel and R, Thomas Baier, Erich Neuwirth, and Michele De Meo

glm2: Fitting Generalized Linear Models with Convergence Problems, Ian C. Marschner

Implementing the Compendium Concept with Sweave and DOCSTRIP, Michael Lundholm

Watch Your Spelling! Kurt Hornik and Duncan Murdoch

Ckmeans.1d.dp: Optimal k-means Clustering in One Dimension by Dynamic Programming, Haizhou Wang and Mingzhou Song

Nonparametric Goodness-of-Fit Tests for Discrete Null Distributions, Taylor B. Arnold and John W. Emerson

Using the Google Visualisation API with R, Markus Gesmann and Diego de Castillo

GrapheR: a Multiplatform GUI for Drawing Customizable Graphs in …

Rainbow: An R Package For Visualizing Functional Time Series, Han Lin Shang

The R Journal

Recent advances in computer technology have tremendously increased the use of functional data, whose graphical representation can be infinite-dimensional curves, images or shapes. This article describes four methods for visualizing functional time series using an R add-on package. These methods are demonstrated using age-specific Australian fertility data from 1921 to 2006 and monthly sea surface temperatures from January 1950 to December 2006.

Using The Google Visualisation Api With R, Markus Gesmann, Diego De Castillo

The R Journal

The googleVis package provides an interface between R and the Google Visualisation API to create interactive charts which can be embedded into web pages. The best known of these charts is probably the Motion Chart, popularised by Hans Rosling in his TED talks. With the googleVis package users can easily create web pages with interactive charts based on R data frames and display them either via the local R HTTPhelp server or within their own sites.

Ckmeans.1d.Dp: Optimal K-Means Clustering In One Dimension By Dynamic Programming, Haizhou Wang, Mingzhou Song

The R Journal

The heuristic k-means algorithm, widely used for cluster analysis, does not guarantee optimality. We developed a dynamic programming algorithm for optimal one-dimensional clustering. The algorithm is implemented as an R package called Ckmeans.1d.dp. We demonstrate its ad vantage in optimality and runtime over the standard iterative k-means algorithm.

Implementing The Compendium Concept With Sweave And Docstrip, Michael Lundholm

The R Journal

This article suggests an implementation of the compendium concept by combining Sweave and the LATEX literate programming environment DOCSTRIP.