Numerical Analysis and Scientific Computing Commons^™

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.

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.

Content-Based Social Network Analysis Of Mailing Lists, Angela Bohn, Ingo Feinerer, Kurt Hornik, Patrick Mair

The R Journal

Social Network Analysis (SNA) provides tools to examine relationships between people. Text Mining (TM) allows capturing the text they produce in Web 2.0 applications, for example, however it neglects their social structure. This paper applies an approach to combine the two methods named “content-based SNA”. Using the R mailing lists, R-help and R-devel, we show how this combination can be used to describe people’s interests and to find out if authors who have similar interests actually communicate. We find that the expected positive relationship between sharing interests and communicating gets stronger as the centrality scores of authors in the communication …

Watch Your Spelling!, Kurt Hornik, Duncan Murdoch

The R Journal

We discuss the facilities in base R for spell checking via Aspell, Hunspell or Ispell, which are useful in particular for conveniently checking the spelling of natural language texts in package Rd files and vignettes. Spell checking performance is illustrated using the Rd files in package stats. This example clearly indicates the need for a domain-specific statistical dictionary. We analyze the results of spell checking all Rd files in all CRAN packages and show how these can be employed for building such a dictionary.

Nonparametric Goodness-Of-Fit Tests For Discrete Null Distributions, Taylor B. Arnold, John W. Emerson

The R Journal

Methodology extending nonparametric goodness-of-fit tests to discrete null distributions has existed for several decades. However, modern statistical software has generally failed to provide this methodology to users. We offer a revision of R’s ks.test() function and a new cvm.test() function that fill this need in the R language for two of the most popular nonparametric goodness-of-fit tests. This paper describes these contributions and provides examples of their usage. Particular attention is given to various numerical issues that arise in their implementation.

Portable C++ For R Packages, Martyn Plummer

The R Journal

Package checking errors are more common on Solaris than Linux. In many cases, these errors are due to non-portable C++ code. This article reviews some commonly recurring problems in C++ code found in R packages and suggests solutions.

Glm2: Fitting Generalized Linear Models With Convergence Problems, Ian C. Marschner

The R Journal

The R function glm uses step-halving to deal with certain types of convergence problems when using iteratively reweighted least squares to fit a generalized linear model. This works well in some circumstances but non-convergence remains a possibility, particularly with a non standard link function. In some cases this is be cause step-halving is never invoked, despite a lack of convergence. In other cases step-halving is invoked but is unable to induce convergence. One remedy is to impose a stricter form of step halving than is currently available in glm, so that the deviance is forced to decrease in every iteration. …

Creating And Deploying An Application With (R)Excel And R, Thomas Baier, Erich Neuwirth, Michele De Meo

The R Journal

We present some ways of using R in Excel and build an example application using the package rpart. Starting with simple interactive use of rpart in Excel, we eventually package the code into an Excel-based application, hiding all details (including R itself) from the end user. In the end, our application implements a service oriented architecture (SOA) with a clean separation of presentation and computation layer

Grapher: A Multiplatform Gui For Drawing Customizable Graphs In R, Maxime Hervé

The R Journal

This article presents GrapheR, a Graphical User Interface allowing the user to draw customizable and high-quality graphs without knowing any R commands. Six kinds of graph are available: histograms, box-and-whisker plots, bar plots, pie charts, curves and scatter plots. The complete process is described with the examples of a bar plot and a scatter plot illustrating the legendary puzzle of African and European swallows’ migrations.

The R Journal (June 2011) 3(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

testthat: Get Started with Testing, Hadley Wickham

Content-Based Social Network Analysis of Mailing Lists, Angela Bohn, Ingo Feinerer, Kurt Hornik, and Patrick Mair

Rmetrics: timeDate Package, Yohan Chalabi, Martin Mächler, and Diethelm Würtz

The digitize Package: Extracting Numerical Data from Scatterplots, Timothée Poisot

Differential Evolution with DEoptim, David Ardia, Kris Boudt, Peter Carl, Katharine M. Mullen, and Brian G. Peterson

rworldmap: A New R Package for Mapping Global Data, Andy South

Cryptographic Boolean Functions with R, Frédéric Lafitte, Dirk Van Heule and Julien Van hamme

Raster Images in R Graphics, Paul Murrell

Probabilistic Weather Forecasting in R, …