Programming Languages and Compilers Commons^™

Rpsftm: An R Package For Rank Preserving Structural Failure Time Models, Annabel Allison, Ian R. White, Simon Bond

The R Journal

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999).

The method is randomisation based and uses only the randomised treatment group, …

Queueing: A Package For Analysis Of Queueing Networks And Models In R, Pedro Cañadilla Jiménez, Yolanda Román Montoya

The R Journal

queueing is a package that solves and provides the main performance measures for both basic Markovian queueing models and single and multiclass product-form queueing networks. It can be used both in education and for professional purposes. It provides an intuitive, straightforward wayto build queueing models using S3 methods. The package solves Markovian models of the form M/M/c/K/M/FCFS, open and closed single class Jackson networks, open and closed multiclass networks and mixed networks. Markovian models are used when both the customer inter-arrival time and the server processing time are exponentially distributed. Queueing network solvers are useful for modelling situations in which …

Crtgeedr: An R Package For Doubly Robust Generalized Estimating Equations Estimations In Cluster Randomized Trials With Missing Data, Melanie Prague, Rui Wang, Victor De Gruttola

The R Journal

Semi-parametric approaches based on generalized estimating equations (GEE) are widely used to analyze correlated outcomes in longitudinal settings. In this paper, we present a package CRTgeeDR developed for cluster randomized trials with missing data (CRTs). For use of inverse probability weighting to adjust for missing data in cluster randomized trials, we show that other software lead to biased estimation for non-independence working correlation structure. CRTgeeDR solves this problem. We also extend the ability of existing packages to allow augmented Doubly Robust GEEestimation (DR). Simulation studies demonstrate the consistency of estimators implemented in CRTgeeDR compared to packages such as geepack and …

Afmtoolkit: An R Package For Automated Afm Force-Distance Curves Analysis, Rafael Benítez, Vicente J. Bolós, José-Luis Toca-Herrera

The R Journal

Atomic force microscopy (AFM) is widely used to measure molecular and colloidal inter actions as well as mechanical properties of biomaterials. In this paper the afmToolkit R package is introduced. This package allows the user to automatically batch process AFM force-distance and force-time curves. afmToolkit capabilities range from importing ASCII files and preprocessing the curves (contact point detection, baseline correction...) for finding relevant physical information, such as Young’s modulus, adhesion energies and exponential decay for force relaxation and creep experiments. This package also contains plotting, summary and feature extraction functions. The package also comes with several data sets so the …

Furniture For Quantitative Scientists, Tyson S. Barrett, Emily Brignone

The R Journal

A basic understanding of the distributions of study variables and the relationships among them is essential to inform statistical modeling. This understanding is achieved through the computation of summary statistics and exploratory data analysis. Unfortunately, this step tends to be under-emphasized in the research process, in part because of the often tedious nature of thorough exploratory data analysis. The table1() function in the furniture package streamlines much of the exploratory data analysis process, making the computation and communication of summary statistics simple and beautiful while offering significant time-savings to the researcher

Openebgm: An R Implementation Of The Gamma-Poisson Shrinker Data Mining Model, Travis Canida, John Ihrie

The R Journal

We introduce the R package openEBGM, an implementation of the Gamma-Poisson Shrinker (GPS) model for identifying unexpected counts in large contingency tables using an empirical Bayes approach. The Empirical Bayes Geometric Mean (EBGM) and quantile scores are obtained from the GPS model estimates. openEBGM provides for the evaluation of counts using a number of different methods, including the model-based disproportionality scores, the relative reporting ratio (RR), and the proportional reporting ratio (PRR). Data squashing for computational efficiency and stratification for confounding variable adjustment are included. Application to adverse event detection is discussed.

An Introduction To Rocker: Docker Containers For R, Carl Boettiger, Dirk Eddelbuettel

The R Journal

We describe the Rocker project, which provides a widely-used suite of Docker images with customized R environments for particular tasks. We discuss how this suite is organized, and how these tools can increase portability, scaling, reproducibility, and convenience of R users and developers.

What Do Developers Search For On The Web?, Xin Xia, Lingfeng Bao, David Lo, Pavneet Singh Kochhar, Ahmed E. Hassan, Zhenchang Xing

Research Collection School Of Computing and Information Systems

Developers commonly make use of a web search engine such as Google to locate online resources to improve their productivity. A better understanding of what developers search for could help us understand their behaviors and the problems that they meet during the software development process. Unfortunately, we have a limited understanding of what developers frequently search for and of the search tasks that they often find challenging. To address this gap, we collected search queries from 60 developers, surveyed 235 software engineers from more than 21 countries across five continents. In particular, we asked our survey participants to rate the …

Software Reengineering: Reverse Engineering With Using 4+1 Architectural Views And Forward Engineering With Mvc Architecture, Shane Mueller

ASA Multidisciplinary Research Symposium

As software complexity is increasing exponentially in our modern era, software architecture becomes increasingly important. The separation of concerns through architecture allows each programmer the opportunity to limit their need of understanding to only the portion of code for which they are responsible for, thus saving large amounts of time.

Sudoku App: Model-Driven Development Of Android Apps Using Ocl?, Yoonsik Cheon, Aditi Barua

Departmental Technical Reports (CS)

Model driven development (MDD) shifts the focus of software development from writing code to building models by developing an application as a series of transformations on models including eventual code generation. Can the key ideas of MDD be applied to the development of Android apps, one of the most popular mobile platforms of today? To answer this question, we perform a small case study of developing an Android app for playing Sudoku puzzles. We use the Object Constraint Language (OCL) as the notation for creating precise models and translate OCL constraints to Android Java code. Our findings are mixed in …

On Locating Malicious Code In Piggybacked Android Apps, Li Li, Daoyuan Li, Tegawende F. Bissyande, Jacques Klein, Haipeng Cai, David Lo, Yves Le Traon

Research Collection School Of Computing and Information Systems

To devise efficient approaches and tools for detecting malicious packages in the Android ecosystem, researchers are increasingly required to have a deep understanding of malware. There is thus a need to provide a framework for dissecting malware and locating malicious program fragments within app code in order to build a comprehensive dataset of malicious samples. Towards addressing this need, we propose in this work a tool-based approach called HookRanker, which provides ranked lists of potentially malicious packages based on the way malware behaviour code is triggered. With experiments on a ground truth of piggybacked apps, we are able to automatically …

A Semantics Comparison Workbench For A Concurrent, Asynchronous, Distributed Programming Language, Claudio Corrodi, Alexander Heußner, Christopher M. Poskitt

Research Collection School Of Computing and Information Systems

A number of high-level languages and libraries have been proposed that offer novel and simple to use abstractions for concurrent, asynchronous, and distributed programming. The execution models that realise them, however, often change over time---whether to improve performance, or to extend them to new language features---potentially affecting behavioural and safety properties of existing programs. This is exemplified by SCOOP, a message-passing approach to concurrent object-oriented programming that has seen multiple changes proposed and implemented, with demonstrable consequences for an idiomatic usage of its core abstraction. We propose a semantics comparison workbench for SCOOP with fully and semi-automatic tools for analysing …

The Impact Of Coverage On Bug Density In A Large Industrial Software Project, Thomas Bach, Artur Andrzejak, Ralf Pannemans, David Lo

Research Collection School Of Computing and Information Systems

Measuring quality of test suites is one of the major challenges of software testing. Code coverage identifies tested and untested parts of code and is frequently used to approximate test suite quality. Multiple previous studies have investigated the relationship between coverage ratio and test suite quality, without a clear consent in the results. In this work we study whether covered code contains a smaller number of future bugs than uncovered code (assuming appropriate scaling). If this correlation holds and bug density is lower in covered code, coverage can be regarded as a meaningful metric to estimate the adequacy of testing. …

Defaultification Refactoring: A Tool For Automatically Converting Java Methods To Default, Raffi Khatchadourian, Hidehiko Masuhara

Publications and Research

Enabling interfaces to declare (instance) method implementations, Java 8 default methods can be used as a substitute for the ubiquitous skeletal implementation software design pattern. Performing this transformation on legacy software manually, though, may be non-trivial. The refactoring requires analyzing complex type hierarchies, resolving multiple implementation inheritance issues, reconciling differences between class and interface methods, and analyzing tie-breakers (dispatch precedence) with overriding class methods. All of this is necessary to preserve type-correctness and confirm semantics preservation. We demonstrate an automated refactoring tool called Migrate Skeletal Implementation to Interface for transforming legacy Java code to use the new default construct. The …

Wrangle Your Data Like A Pro With The Data Processing Power Of Python, Geoffrey P. Timms, Jeremy M. Brown

Charleston Library Conference

Management, delivery, and marketing of library resources and collections necessitate interaction with a plethora of data from many sources and in many forms. Accessing and transforming data into meaningful information or different formats used in library automation can be time consuming, but a working knowledge of a programming language can improve efficiency in many facets of librarianship. From processing lists to creating extensible markup language (XML), from editing machine-readable cataloging (MARC) records before upload to automating statistical reports, the Python programming language and third-party application programming interfaces (APIs) can be used to accomplish both behind-the-scenes tasks and end-user facing projects. …

Distributed Evolution Of Spiking Neuron Models On Apache Mahout For Time Series Analysis, Andrew Palumbo

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Fastshrinkage: Perceptually-Aware Retargeting Toward Mobile Platforms, Zhenguang Liu, Zepeng Wang, Luming Zhang, Rajiv Ratn Shah, Yingjie Xia, Yi Yang, Wei Liu

Research Collection School Of Computing and Information Systems

Retargeting aims at adapting an original high-resolution photo/video to a low-resolution screen with an arbitrary aspect ratio. Conventional approaches are generally based on desktop PCs, since the computation might be intolerable for mobile platforms (especially when retargeting videos). Besides, only low-level visual features are exploited typically, whereas human visual perception is not well encoded. In this paper, we propose a novel retargeting framework which fast shrinks photo/video by leveraging human gaze behavior. Specifically, we first derive a geometry-preserved graph ranking algorithm, which efficiently selects a few salient object patches to mimic human gaze shifting path (GSP) when viewing each scenery. …

Joanaudit: A Tool For Auditing Common Injection Vulnerabilities, Julian Thome, Lwin Khin Shar, Domenico Bianculli, Lionel Briand

Research Collection School Of Computing and Information Systems

JoanAudit is a static analysis tool to assist security auditors in auditing Web applications and Web services for common injection vulnerabilities during software development. It automatically identifies parts of the program code that are relevant for security and generates an HTML report to guide security auditors audit the source code in a scalable way. JoanAudit is configured with various security-sensitive input sources and sinks relevant to injection vulnerabilities and standard sanitization procedures that prevent these vulnerabilities. It can also automatically fix some cases of vulnerabilities in source code — cases where inputs are directly used in sinks without any form …

Evaluating Student Perceptions And Learning Outcomes: Differences Between Sla-Able And Non-Sla-Able Introductory Programming Courses, Christina M. Frederick, Matthew B. Pierce, Andrew Griggs, Lulu Sun

Publications

Engineering, computer science and subsequently knowledge of programming language is an increasingly vital skill in today’s workforce. First year engineering students are introduced to programming in addition to rigorous course loads in their first year. Second Language Acquisition (SLA) has been applied to programming course content delivery and has shown promise as an effective means of better educating new students. Results will be presented from a NSF funded study conducted over the past two years. SLA was applied to an introductory engineering course that teaches basic programming skills in a Blended learning environment (SLA-aBLe). This study examined four semesters worth …

Code Coverage And Postrelease Defects: A Large-Scale Study On Open Source Projects, Pavneet Singh Kochhar, David Lo, Julia Lawall, Nachiappan Nagappan

Research Collection School Of Computing and Information Systems

Testing is a pivotal activity in ensuring the quality of software. Code coverage is a common metric used as a yardstick to measure the efficacy and adequacy of testing. However, does higher coverage actually lead to a decline in postrelease bugs? Do files that have higher test coverage actually have fewer bug reports? The direct relationship between code coverage and actual bug reports has not yet been analyzed via a comprehensive empirical study on real bugs. Past studies only involve a few software systems or artificially injected bugs (mutants). In this empirical study, we examine these questions in the context …