Numerical Analysis and Scientific Computing Commons^™

Asymptest: A Simple R Package For Classical Parametric Statistical Tests And Confidence Intervals In Large Samples, J.-F. Coeurjolly, R. Drouilhet, P. Lafaye De Micheaux, J.-F. Robineau

The R Journal

asympTest is an R package implementing large sample tests and confidence intervals. One and two sample mean and variance tests (differences and ratios) are considered. The test statistics are all expressed in the same form as the Student t-test, which facilitates their presentation in the classroom. This contribution also fills the gap of a robust (to non-normality) alternative to the chi-square single variance test for large samples, since no such procedure is implemented in standard statistical software.

Convergenceconcepts: An R Package To Investigate Various Modes Of Convergence, Pierre Lafaye De Micheaux, Benoit Liquet

The R Journal

ConvergenceConcepts is an R pack age, built upon the tkrplot, tcltk and lattice packages, designed to investigate the convergence of simulated sequences of random variables. Four classical modes of convergence may be studied, namely: almost sure convergence (a.s.), convergence in probability (P), convergence in law (L) and convergence in r-th mean (r). This investigation is performed through ac curate graphical representations. This package may be used as a pedagogical tool. It may give students a better understanding of these notions and help them to visualize these difficult theoretical concepts. Moreover, …

The R Journal (December 2009) 1(2): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Aspects of the Social Organization and Trajectory of the R Project, John Fox

Party on! Carolin Strobl, Torsten Hothorn and Achim Zeileis

ConvergenceConcepts: An R Package to Investigate Various Modes of Convergence, Pierre Lafaye de Micheaux and Benoit Liquet

asympTest: A Simple R Package for Classical Parametric Statistical Tests and Confidence Intervals in Large Samples, J.-F. Coeurjolly, R. Drouilhet, P. Lafaye de Micheaux and J.-F. Robineau

copas: An R package for Fitting the Copas Selection Model, J. Carpenter, G. Rücker and G. Schwarzer

Transitioning to R: Replicating SAS, Stata, and SUDAAN Analysis Techniques in Health Policy Data, …

Sample Size Estimation While Controlling False Discovery Rate For Microarray Experiments Using The Ssize.Fdr Package, Megan Orr, Peng Liu

The R Journal

Microarray experiments are becoming more and more popular and critical in many biological disciplines. As in any statistical experiment, appropriate experimental design is essential for reliable statistical inference, and sample size has a crucial role in experimental design. Because microarray experiments are rather costly, it is important to have an adequate sample size that will achieve a desired power with out wasting resources.

For a given microarray data set, thousands of hypotheses, one for each gene, are simultaneously tested. Storey and Tibshirani (2003) argue that con trolling false discovery rate (FDR) is more reasonable and more powerful than controlling family-wise …

Emd: A Package For Empirical Mode Decomposition And Hilbert Spectrum, Donghoh Kim, Hee-Seok Oh

The R Journal

The concept of empirical mode decomposition (EMD)and the Hilber tspectrum (HS) has been developed rapidly in many disciplines of science and engineering since Huang et al. (1998) invented EMD. The key feature of EMD is to decompose a signal into so-called intrinsic mode function (IMF). Further more, the Hilbert spectral analysis of intrinsic mode functions provides frequency information evolving with time and quantifies the amount of variation due to oscillation at different time scales and time locations. In this article,we introduce an R package called EMD (KimandOh, 2008) that performs one and two-dimensional EMD and HS.

Modeling Without Data Using Expert Opinion, Vincent Goulet, Michel Jacques, Mathieu Pigeon

The R Journal

The expert package provides tools to create and manipulate empirical statistical models using expert opinion (or judgment). Here, the latter expression refers to a specific body of techniques to elicit the distribution of a random variable when data is scarce or unavailable. Opinions on the quantiles of the distribution are sought from experts in the field and aggregated into a final estimate. The package supports aggregation by means of the Cooke, Mendel–Sheridan and predefined weights models.

We do not mean to give a complete introduction to the theory and practice of expert opinion elicitation in this paper. However, for the …

Admit, David Ardia, Lennart F. Hoogerheide, Herman K. Van Dijk

The R Journal

This note presents the package AdMit (Ardia et al., 2008, 2009), an R implementation of the adaptive mixture of Student-t distributions (AdMit) procedure developed by Hoogerheide (2006); see also Hoogerheide et al. (2007); Hoogerheide and van Dijk (2008). The AdMit strategy consists of the construction of a mixture of Student-t distributions which approximates a target distribution of interest. The fitting procedure relies only on a kernel of the tar get density, so that the normalizing constant is not required. In a second step, this approximation is used as an importance function in importance sampling or as a candidate density in …

The Hwriter Package: Composing Html Documents With R Objects, Gregoire Pau, Wolfgang Huber

The R Journal

HTML documents are structured documents made of diverse elements such as paragraphs, sections, columns, figures and tables organized in a hierarchical layout. Combination of HTML documents and hyperlinking is useful to report analysis results; for example, in the package array Quality Metrics (Kauffmannetal., 2009), estimating the quality of mi croarray data sets and cellHTS2(Boutrosetal.,2006), performing the analysis of cell-based screens.

There are several tools for exporting data from R into HTML documents. The package R2HTML is able to render a large diversity of R objects in HTML but does not easily support combining them in a structured layout and …

Collaborative Software Development Using R-Forge, Stefan Theußl, Achim Zeileis

The R Journal

Open source software (OSS) is typically created in a decentralized self-organizing process by a community of developers having the same or similar interests (see the famous essay by Raymond, 1999). A key factor for the success of OSS over the last two decades is the Internet: Developers who rarely meet face-to-face can employ new means of communication, both for rapidly writing and deploying software (in the spirit of Linus Torvald’s “release early, release often paradigm”). Therefore, many tools emerged that assist a collaborative software development process, including in particular tools for source code management (SCM) and version control.

In the …

Facets Of R, John M. Chambers

The R Journal

We are seeing today a widespread, and welcome, tendency for non-computer-specialists among statisticians and others to write collections of R functions that organize and communicate their work. Along with the flood of software sometimes comes an attitude that one need-only-learn, or teach, a sort of basic how-to-write-the-function level of R programming, beyond which most of the detail is unimportant or can be absorbed without much discussion. As delusions go, this one is not very objectionable if it encourages participation. Nevertheless, a delusion it is. In fact, functions are only one of a variety of important facets that R has acquired …

Easier Parallel Computing In R With Snowfall And Sfcluster, Jochen Knaus, Christine Porzelius, Harald Binder, Guido Schwarzer

The R Journal

Many statistical analysis tasks in areas such as bioinformatics are computationally very intensive, while lots of them rely on embarrassingly parallel computations (Grama et al., 2003). Multiple computers or even multiple processor cores on standard desktop computers, which are widespread nowadays, can easily contribute to faster analyses.

R itself does not allow parallel execution. There are some existing solutions for R to distribute calculations over many computers — a cluster — for ex ample Rmpi, rpvm, snow, nws or papply. However these solutions require the user to setup and manage the cluster on his own and …

The R Journal (June 2009) 1(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Facets of R, John M. Chambers

Collaborative Software Development Using R-Forge, Stefan Theußl and Achim Zeileis

Drawing Diagrams with R, Paul Murrell

The hwriter package: Composing HTML Documents with R Objects, Gregoire Pau and Wolfgang Huber

AdMit, David Ardia, Lennart F. Hoogerheide, and Herman K. van Dijk

expert: Modeling Without Data Using Expert Opinion, Vincent Goulet, Michel Jacques, and Mathieu Pigeon

New Numerical Algorithm for Multivariate Normal Probabilities in Package mvtnorm, Xuefei Mi, Tetsuhisa Miwa, and Torsten Hothorn

EMD: A Package for Empirical Mode Decomposition and Hilbert Spectrum, Donghoh Kim, and Hee-Seok Oh

Sample Size Estimation while …

Drawing Diagrams With R, Paul Murrell

The R Journal

R provides a number of well-known high-level facilities for producing sophisticated statistical plots, including the “traditional” plots in the graphics pack age (R Development Core Team, 2008), the Trellis style plots provided by lattice (Sarkar, 2008), and the grammar-of-graphics-inspired approach of ggplot2 (Wickham, 2009). However, R also provides a powerful set of low level graphics facilities for drawing basic shapes and, more importantly, for arranging those shapes relative to each other, which can be used to draw a wide variety of graphical images. This article highlights some of R’s low-level graphics facilities by demonstrating their use in the production of …

Pmml: An Open Standard For Sharing Models, Alex Guazzelli, Michael Zeller, Wen-Ching Lin, Graham Williams

The R Journal

The PMML package exports a variety of predictive and descriptive models from R to the Predictive Model Markup Language (Data Mining Group, 2008). PMML is an XML-based language and has become the de-facto standard to represent not only predictive and descriptive models, but also data pre- and post-processing. In so doing, it allows for the interchange of models among different tools and environments, mostly avoiding proprietary issues and incompatibilities.

The PMML package itself (Williams et al., 2009) was conceived at first as part of Togaware’s data mining toolkit Rattle, the R Analytical Tool To Learn Easily (Williams, 2009). Although it …

User Interface Design, Moritz Stefaner, Sebastien Ferre, Saverio Perugini, Jonathan Koren, Yi Zhang

Computer Science Faculty Publications

As detailed in Chap. 1, system implementations for dynamic taxonomies and faceted search allow a wide range of query possibilities on the data. Only when these are made accessible by appropriate user interfaces, the resulting applications can support a variety of search, browsing and analysis tasks. User interface design in this area is confronted with specific challenges. This chapter presents an overview of both established and novel principles and solutions.

Link Lifetimes And Randomized Neighbor Selection In Dhts, Zhongmei Yao, Dmitri Loguinov

Computer Science Faculty Publications

Several models of user churn, resilience, and link lifetime have recently appeared in the literature [12], [13], [34], [35]; however, these results do not directly apply to classical Distributed Hash Tables (DHTs) in which neighbor replacement occurs not only when current users die, but also when new user arrive into the system, and where replacement choices are often restricted to the successor of the failed zone in the DHT space. To understand neighbor churn in such networks, this paper proposes a simple, yet accurate, model for capturing link dynamics in structured P2P systems and obtains the distribution of link lifetimes …

Performance Analysis Of Ieee 802.11b Devices In The Presence Of Interference Aware Scheduling-Adaptive Frequency Hopping Enabled Bluetooth Devices, Deepthi Gopalpet

Electrical & Computer Engineering Theses & Dissertations

Wireless Local Area networks (WLAN) and Wireless Personal Area Networks (WPAN) provide complimentary services using the same unlicensed radio frequency band of operation. The 802.11b WLAN operates in the 2.4 GHz band and uses a Direct Sequence Spread Spectrum technique. It is designed to cover large areas ranging up to 100 meters in diameter, which may connect hundreds of computers. Bluetooth (BT) WPAN also operates in the same frequency band as the IEEE 802.lib and it uses a Frequency Hopping Spread Spectrum technique. BT is primarily used for communications between notebooks, palm units and other personal computing devices within relatively …

Modeling Heterogeneous User Churn And Local Resilience Of Unstructured P2p Networks, Zhongmei Yao, Derek Leonard, Dmitri Loguinov, Xiaoming Wang

Computer Science Faculty Publications

Previous analytical results on the resilience of unstructured P2P systems have not explicitly modeled heterogeneity of user churn (i.e., difference in online behavior) or the impact of in-degree on system resilience. To overcome these limitations, we introduce a generic model of heterogeneous user churn, derive the distribution of the various metrics observed in prior experimental studies (e.g., lifetime distribution of joining users, joint distribution of session time of alive peers, and residual lifetime of a randomly selected user), derive several closed-form results on the transient behavior of in-degree, and eventually obtain the joint in/out degree isolation probability as a simple …

Automatically Discovering The Number Of Clusters In Web Page Datasets, Zhongmei Yao

Computer Science Faculty Publications

Clustering is well-suited for Web mining by automatically organizing Web pages into categories, each of which contains Web pages having similar contents. However, one problem in clustering is the lack of general methods to automatically determine the number of categories or clusters. For the Web domain in particular, currently there is no such method suitable for Web page clustering. In an attempt to address this problem, we discover a constant factor that characterizes the Web domain, based on which we propose a new method for automatically determining the number of clusters in Web page data sets. We discover that the …

Development Of A Systems Engineering Model For Chemical Separation Process, Lijian Sun

UNLV Theses, Dissertations, Professional Papers, and Capstones

This thesis is concerned with the efforts to develop a general-purpose systems engineering model software TRPSEMPro1 that can be used to improve productivity in the design process. Different features of TRPSEMPro will be presented in this thesis. First, Systems Engineering technology is presented, followed by the exposition of different numerical optimization technologies and DOE (Design of Experiments) study technologies. Second, the detailed software process, Object-Oriented Analysis and Design (OOA&D) for the TRPSEMPro is presented. All the design data models are expressed by using Unified Modeling Language (UML).

AMUSESimulator is another software package which has been designed and implemented in order …

Personalizing Interactions With Information Systems, Saverio Perugini, Naren Ramakrishnan

Computer Science Faculty Publications

Personalization constitutes the mechanisms and technologies necessary to customize information access to the end-user. It can be defined as the automatic adjustment of information content, structure, and presentation tailored to the individual. In this chapter, we study personalization from the viewpoint of personalizing interaction. The survey covers mechanisms for information-finding on the web, advanced information retrieval systems, dialog-based applications, and mobile access paradigms. Specific emphasis is placed on studying how users interact with an information system and how the system can encourage and foster interaction. This helps bring out the role of the personalization system as a facilitator which reconciles …

The Partial Evaluation Approach To Information Personalization, Naren Ramakrishnan, Saverio Perugini

Computer Science Faculty Publications

Information personalization refers to the automatic adjustment of information content, structure, and presentation tailored to an individual user. By reducing information overload and customizing information access, personalization systems have emerged as an important segment of the Internet economy. This paper presents a systematic modeling methodology— PIPE (‘Personalization is Partial Evaluation’) — for personalization. Personalization systems are designed and implemented in PIPE by modeling an information-seeking interaction in a programmatic representation. The representation supports the description of information-seeking activities as partial information and their subsequent realization by partial evaluation, a technique for specializing programs. We describe the modeling methodology at a …

Visualizing Electrostatic Phenomena Using Mathematica, Eric Mayes

Journal of the Arkansas Academy of Science

A set of packages for visualizing electrostatic phenomena was developed using Mathematica as a programming language. These packages allow users to plot potential fields, equipotential lines, 2-D and 3-D vector fields in order to gain a visual understanding of electrostatic charges. They would be useful in accompanying undergraduate physics labs pertaining to electrostatics, as they would enable students to connect experiment with mathematics through open-ended visual exploration