Programming Languages and Compilers Commons^™

The R User Conference 2013, User 2013 Organising Committee

The R Journal

The ninth R user conference will take place at the University of Castilla-La Mancha, Albacete, Spain from Wednesday 10 July 2013 to Friday 12 July 2013. Following previous useR! conferences, this meeting of the R user community will

• focus on R as the ‘lingua franca’ of data analysis and statistical computing;
• provide a platform for R users to discuss and exchange ideas on how R can be used for statistical computation, data analysis, visualization and exciting applications in various fields;
• give an overview of the new features of the ever evolving R project.

Ftsa: An R Package For Analyzing Functional Time Series, Han Lin Shang

The R Journal

Recent advances in computer recording and storing technology have tremendously increased the presence of functional data, whose graphical representation can be infinite-dimensional curve, image, or shape. When the same functional object is observed over a period of time, such data are known as functional time series. This article makes first attempt to describe several techniques (centered around functional principal component analysis) for modeling and forecasting functional time series from a computational aspect, using a readily-available R addon package. These methods are demonstrated using age-specific Australian fertility rate data from 1921 to 2006, and monthly sea surface temperature data from January …

An Introduction To The Ecotroph R Package: Analyzing Aquatic Ecosystem Trophic Networks, Mathieu Colléter, Jérôme Guitton, Didier Gascuel

The R Journal

Recent advances in aquatic ecosystem modelling have particularly focused on trophic network analysis through trophodynamic models. We present here a R package devoted to a recently developed model, EcoTroph. This model enables the analysis of aquatic ecological networks and the related impacts of fisheries. It was available through a plug-in in the well-known Ecopath with Ecosim software or through implementations in Excel sheets. The R package we developed simplifies the access to the EcoTroph model and offers a new interfacing between two widely used software, Ecopath and R.

Fast Pure R Implementation Of Gee: Application Of The Matrix Package, Lee S. Mcdaniel, Nicholas C. Henderson, Paul J. Rathouz

The R Journal

Generalized estimating equation solvers in R only allow for a few pre-determined options for the link and variance functions. We provide a package, geeM, which is implemented entirely in R and allows for user specified link and variance functions. The sparse matrix representations provided in the Matrix package enable a fast implementation. To gain speed, we make use of analytic inverses of the working correlation when possible and a trick to find quick numeric inverses when an analytic inverse is not available. Through three examples, we demonstrate the speed of geeM, which is not much worse than C …

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

Mind Change Speed-Up For Learning Languages From Positive Data, Sanjay Jain, Efim Kinber

School of Computer Science & Engineering Faculty Publications

Within the frameworks of learning in the limit of indexed classes of recursive languages from positive data and automatic learning in the limit of indexed classes of regular languages (with automatically computable sets of indices), we study the problem of minimizing the maximum number of mind changes by a learner on all languages with indices not exceeding . For inductive inference of recursive languages, we establish two conditions under which can be made smaller than any recursive unbounded non-decreasing function. We also establish how is affected if at least one of these two conditions does not hold. In the case …

Spring­11: Pdc In Cs1/2 And A Mobile/Cloud Intermediate Mobile/Cloud Intermediate Software Design Course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Recent changes in the environment of Loyola University Chicago’s Department of Computer Science include a better differentiation of our four undergraduate majors, growing interest in computing among science majors, and an increased demand for graduates with mobile and cloud skills. In our continued effort to incorporate parallel and distributed computing topics into the undergraduate curriculum, we are focusing on these three existing courses:

CS1: In response to a request from the physics department, we started to offer a CS1 section aimed at majors in physics and other hard sciences this spring semester. This section includes some material on numerical methods …

Building Capable, Energy-Efficient, Flexible Visualization And Sensing Clusters From Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

We explore the application of clusters of commodity tablet devices to problems spanning a “trilogy” of concerns: visualization, sensing, and computation. We conjecture that such clusters provide a low-cost, energy-efficient, flexible, and ultimately effective platform to tackle a wide range of problems within this trilogy. This is a work in progress, and we now elaborate our position and give a preliminary status report.

A wide range of Android tablet devices are available in terms of price and capabilities. “You get what you pay for” w.r.t. display resolution, sensors, and chipset---corresponding to the trilogy. $200 gets one a 1280x800-pixel touch display, …

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Distortion Tolerant Source Code Using Viterbi Algorithm, Christopher Hankins

Electrical Engineering Undergraduate Honors Theses

Convolutional codes are used in digital communication systems in order to protect information from distortion and increase system reliability. One of the most efficient methods for decoding convolutional codes is based on the Viterbi Algorithm. Considering the fundamental similarities between these channel codes and source codes, it is logical to postulate that the Viterbi Algorithm may also provide a basis for the implementation of an efficient lossy source code. In this thesis, the Viterbi Algorithm is used to used to compress digital data from a symmetric Bernoulli source. The Viterbi source code is simulated and shown to produce results which …

Cjc: An Extensible Checker For The Cleanjava Annotation Language, Cesar Yeep

Departmental Technical Reports (CS)

CleanJava is a formal annotation language for the Java programming language to support a Cleanroom-style functional program verification technique that views programs as mathematical functions. It needs a suite of support tools including a checker that can parse annotations and check them for syntactic and static semantic correctness. The two key requirements of the checker are flexibility and extensibility. Since the language is still under development and refinement, it should be flexible to facilitate language experimentation and accommodate language changes. It should be also extensible to provide base code for developing more advanced support tools like an automated theorem prover. …

Efficient Architectures For Retrieving Mixed Data With Rest Architecture Style And Html5 Support, Koushik Maddipudi

Masters Theses & Specialist Projects

Software as a service is an emerging but important aspect of the web. Web
Services play a vital role in providing it. Web Services are commonly provided in one of two architectural styles: a "REpresentational State Transfer" (REST), or using the "Simple Object Access Protocol" (SOAP.) Originally most web content was text and small images. But more recent services involve complex data structures including text, images, audio, and video. The task of optimizing data to provide delivery of these structures is a complex one, involving both theoretical and practical aspects. In this thesis work, I have considered two architectures developed …

Tower Of Babel: A Crowdsourcing Game Building Sentiment Lexicons For Resource-Scarce Languages, Yoonsung Hong, Haewoon Kwak, Youngmin Baek, Sue. Moon

Research Collection School Of Computing and Information Systems

With the growing amount of textual data produced by online social media today, the demands for sentiment analysis are also rapidly increasing; and, this is true for worldwide. However, non-English languages often lack sentiment lexicons, a core resource in performing sentiment analysis. Our solution, Tower of Babel (ToB), is a language-independent sentiment-lexicon-generating crowdsourcing game. We conducted an experiment with 135 participants to explore the difference between our solution and a conventional manual annotation method. We evaluated ToB in terms of effectiveness, efficiency, and satisfactions. Based on the result of the evaluation, we conclude that sentiment classification via ToB is accurate, …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Senior Project Report - Doctest, Stephen Weessies

Computer Engineering

DocTest is a program that, simply put, allows a programmer or user to document STANAG 4586 (a standard for unmanned aerial vehicle interoperability) messages and test the vehicle system at Lockheed Martin [5]. The program is extensible to allow for further development aiding our software team to do what they do best and not get bogged down in tedious but necessary documentation. DocTest is also used to aid in testing, keeping track of the issues and bugs found and creating a document that captures each issue so an issue is not missed or forgotten. This program was made for use …

Object-Oriented Programming: Some History, And Challenges For The Next Fifty Years, Andrew P. Black

Computer Science Faculty Publications and Presentations

Object-oriented programming is inextricably linked to the pioneering work of Ole-Johan Dahl and Kristen Nygaard on the design of the Simula language, which started at the Norwegian Computing Centre in the Spring of 1961. However, object-orientation, as we think of it today—fifty years later—is the result of a complex interplay of ideas, constraints and people. Dahl and Nygaard would certainly recognize it as their progeny, but might also be amazed at how much it has grown up. This article is based on a lecture given on 22nd August 2011, on the occasion of the scientific opening of the Ole-Johan …

Constructing Verifiably Correct Java Programs Using Ocl And Cleanjava, Yoonsik Cheon, Carmen Avila

Departmental Technical Reports (CS)

A recent trend in software development is building a precise model that can be used as a basis for the software development. Such a model may enable an automatic generation of working code, and more importantly it provides a foundation for correctness reasoning of code. In this paper we propose a practical approach for constructing a verifiably correct program from such a model. The key idea of our approach is (a) to systematically translate formally-specified design constraints such as class invariants and operation pre and postconditions to code-level annotations and (b) to use the annotations for the correctness proof of …

Verifying Linearizability Via Optimized Refinement Checking, Yang Liu, Wei Chen, Yanhong A. Liu, Jun Sun, Shao Jie Zhang, Jin Song Dong Dong

Research Collection School Of Computing and Information Systems

Linearizability is an important correctness criterion for implementations of concurrent objects. Automatic checking of linearizability is challenging because it requires checking that: 1) All executions of concurrent operations are serializable, and 2) the serialized executions are correct with respect to the sequential semantics. In this work, we describe a method to automatically check linearizability based on refinement relations from abstract specifications to concrete implementations. The method does not require that linearization points in the implementations be given, which is often difficult or impossible. However, the method takes advantage of linearization points if they are given. The method is based on …

Modeling And Verifying Hierarchical Real-Time Systems Using Stateful Timed Csp, Jun Sun, Yang Liu, Jin Song Dong, Yan Liu, Ling Shi, Étienne André

Research Collection School Of Computing and Information Systems

Modeling and verifying complex real-time systems are challenging research problems. The de facto approach is based on Timed Automata, which are finite state automata equipped with clock variables. Timed Automata are deficient in modeling hierarchical complex systems. In this work, we propose a language called Stateful Timed CSP and an automated approach for verifying Stateful Timed CSP models. Stateful Timed CSP is based on Timed CSP and is capable of specifying hierarchical real-time systems. Through dynamic zone abstraction, finite-state zone graphs can be generated automatically from Stateful Timed CSP models, which are subject to model checking. Like Timed Automata, Stateful …

Modules And Dialects As Objects In Grace, Michael Homer, James Noble, Kim B. Bruce, Andrew P. Black

Computer Science Faculty Publications and Presentations

Grace is a gradually typed, object-oriented language for use in education; consonant with that use, we have tried to keep Grace as simple and straightforward as possible. Grace needs a module system for several reasons: to teach students about modular program design, to organise large programs, especially its self-hosted implementation, to provide access to resources defined in other languages, and to support different “dialects”—language subsets, or domain specific languages, for particular parts of the curriculum. Grace already has several organising constructs; this paper describes how Grace uses two of them, objects and lexical scope, to provide modules and dialects.

Interactive Ambient Visualizations For Soft Advice, Emerson Murphy-Hill, Titus Barik, Andrew P. Black

Computer Science Faculty Publications and Presentations

Some software packages offer the user soft advice: recommendations that are intended to help the user create high quality artifacts, but which may turn out to be bad advice. It is left to the user to determine whether the soft advice really will improve quality, and to decide whether or not to adopt it. Visualizations can help the user in making this decision, but we believe that conventional visualizations are less than ideal. In this paper, we describe an interactive ambient visualization to help users identify, understand and interpret soft advice.

Our visualization was developed to help programmers interpret code …

The Grace Programming Language Draft Specification Version 0.3.1261, Andrew P. Black, Kim B. Bruce, James Noble

Computer Science Faculty Publications and Presentations

This is a specification of the Grace Programming Language. This specification is notably incomplete, and everything is subject to change.