Computer Sciences Commons^™

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

CRAN growth

New CRAN task views

New packages in CRAN task views

Easyroc: An Interactive Web-Tool For Roc Curve Analysis Using R Language Environment, Dincer Goksuluk, Selcuk Korkmaz, Gokmen Zararsiz, A Ergun Karaagaoglu

The R Journal

ROC curve analysis is a fundamental tool for evaluating the performance of a marker in a number of research areas, e.g., biomedicine, bioinformatics, engineering etc., and is frequently used for discriminating cases from controls. There are a number of analysis tools which are used to guide researchers through their analysis. Some of these tools are commercial and provide basic methods for ROC curve analysis while others offer advanced analysis techniques and a command-based user interface, such as the R environment. The R environment includes comprehensive tools for ROC curve analysis; however, using a command-based interface might be challenging and time …

Hdm: High-Dimensional Metrics, Victor Chernozhukov, Chris Hansen, Martin Spindler

The R Journal

In this article the package High-dimensional Metrics hdm is introduced. It is a collection of statistical methods for estimation and quantification of uncertainty in high-dimensional approximately sparse models. It focuses on providing confidence intervals and significance testing for (possibly many) low-dimensional subcomponents of the high-dimensional parameter vector. Efficient estimators and uniformly valid confidence intervals for regression coefficients on target variables (e.g., treatment or policy variable) in a high-dimensional approximately sparse regression model, for average treatment effect (ATE) and average treatment effect for the treated (ATET), as well for extensions of these param eters to the endogenous setting are provided. Theory …

Distance Measures For Time Series In R: The Tsdist Package, Usue Mori, Alexander Mendiburu, Jose A. Lozano

The R Journal

The definition of a distance measure between time series is crucial for many time series data mining tasks, such as clustering and classification. For this reason, a vast portfolio of time series distance measures has been published in the past few years. In this paper, the TSdist package is presented, a complete tool which provides a unified framework to calculate the largest variety of time series dissimilarity measures available in R at the moment, to the best of our knowledge. The package implements some popular distance measures which were not previously available in R, and moreover, it also provides wrappers …

Condsurv: An R Package For The Estimation Of The Conditional Survival Function For Ordered Multivariate Failure Time Data, Luis Meira-Machado, Meira-Machado Sestelo

The R Journal

One major goal in clinical applications of time-to-event data is the estimation of survival with censored data. The usual nonparametric estimator of the survival function is the time-honored Kaplan-Meier product-limit estimator. Though this estimator has been implemented in several R packages, the development of the condSURV R package has been motivated by recent contributions that allow the estimation of the survival function for ordered multivariate failure time data. The condSURV package provides three different approaches all based on the Kaplan-Meier estimator. In one of these approaches these quantities are estimated conditionally on current or past covariate measures. Illustration of the …

Measurement Units In R, Edzer Pebesma, Thomas Mailund, James Hiebert

The R Journal

We briefly review SI units, and discuss R packages that deal with measurement units, their compatibility and conversion. Built upon udunits2 and the UNIDATA udunits library, we introduce the package units that provides a class for maintaining unit metadata. When used in expression, it automatically converts units, and simplifies units of results when possible; in case of incompatible units, errors are raised. The class flexibly allows expansion beyond predefined units. Using units may eliminate a whole class of potential scientific programming mistakes. We discuss the potential and limitations of computing with explicit units.

Tigris: An R Package To Access And Work With Geographic Data From The Us Census Bureau, Kyle Walker

The R Journal

TIGER/Line shapefiles from the United States Census Bureau are commonly used for the mapping and analysis of US demographic trends. The tigris package provides a uniform interface for R users to download and work with these shapefiles. Functions in tigris allow R users to request Census geographic datasets using familiar geographic identifiers and return those datasets as objects of class "Spatial*DataFrame". In turn, tigris ensures consistent and high-quality spatial data for R users’ cartographic and spatial analysis projects that involve US Census data. This article provides an overview of the functionality of the tigris package, and concludes with an applied …

Mixtox: An R Package For Mixture Toxicity Assessment, Xiang-Wei Zhu, Jian-Yi Chen

The R Journal

Mixture toxicity assessment is indeed necessary for humans and ecosystems that are continually exposed to a variety of chemical mixtures. This paper describes an R package, called mixtox, which offers a general framework of curve fitting, mixture experimental design, and mixture toxicity prediction for practitioners in toxicology. The unique features of mixtox include: (1) constructing a uniform table for mixture experimental design; and (2) predicting toxicity of a mixture with multiple components based on reference models such as concentration addition, independent action, and generalized concentration addition. We describe the various functions of the package and provide examples to illustrate their …

Water: Tools And Functions To Estimate Actual Evapotranspiration Using Land Surface Energy Balance Models In R, Guillermo Federico Olmedo, Samuel Ortega-Farías, Daniel De La Fuente-Sáiz, David Fonseca- Luego, Fernando Fuentes-Peñailillo

The R Journal

The crop water requirement is a key factor in the agricultural process. It is usually estimated throughout actual evapotranspiration (ETa). This parameter is the key to develop irrigation strategies, to improve water use efficiency and to understand hydrological, climatic, and ecosystem processes. Currently, it is calculated with classical methods, which are difficult to extrapolate, or with land surface energy balance models (LSEB), such as METRIC and SEBAL, which are based on remote sensing data. This paper describes water, an open implementation of LSEB. The package provides several functions to estimate the parameters of the LSEB equation from satellite data …

Just In Time Assembly (Jita) - A Run Time Interpretation Approach For Achieving Productivity Of Creating Custom Accelerators In Fpgas, Sen Ma

Graduate Theses and Dissertations

The reconfigurable computing community has yet to be successful in allowing programmers to access FPGAs through traditional software development flows. Existing barriers that prevent programmers from using FPGAs include: 1) knowledge of hardware programming models, 2) the need to work within the vendor specific CAD tools and hardware synthesis. This thesis presents a series of published papers that explore different aspects of a new approach being developed to remove the barriers and enable programmers to compile accelerators on next generation reconfigurable manycore architectures. The approach is entitled Just In Time Assembly (JITA) of hardware accelerators. The approach has been defined …

Towards Using Concurrent Java Api Correctly, Shuang Liu, Guangdong Bai, Jun Sun, Jin Song Dong

Research Collection School Of Computing and Information Systems

Concurrent Programs are hard to analyze or debug due to the complex program logic and unpredictable execution environment. In practice, ordinary programmers often adopt existing well-designed concurrency related API (e.g., those in java.util.concurrent) so as to avoid dealing with these issues. These API can however often be used incorrectly, which results in hardto-debug concurrent bugs. In this work, we propose an approach for enforcing the correct usage of concurrency-related Java API. Our idea is to annotate concurrency-related Java classes with annotations related to misuse of these API and develop lightweight type checker to detect concurrent API misuse based on the …

Writing Jml Specifications Using Java 8 Streams, Yoonsik Cheon, Zejing Cao, Khandoker Rahad

Departmental Technical Reports (CS)

JML is a formal behavioral interface specification language for Java to document Java program modules such as classes and interfaces. When composing JML specifications, one frequently writes assertions involving a collection of values. In this paper we propose to use Java 8 streams for writing more concise and cleaner assertions on a collection. The use of streams in JML can be minimal and non-invasive in the conventional style of writing assertions. It can also be holistic to write all assertions in the abstract state defined by streams. We perform a small case study to illustrate our approach and show its …

Service Adaptation With Probabilistic Partial Models, Manman Chen, Tian Huat Tan, Jun Sun, Jingyi Wang, Yang Liu, Jing Sun, Jin Song Dong

Research Collection School Of Computing and Information Systems

Web service composition makes use of existing Web services to build complex business processes. Non-functional requirements are crucial for the Web service composition. In order to satisfy non-functional requirements when composing a Web service, one needs to rely on the estimated quality of the component services. However, estimation is seldom accurate especially in the dynamic environment. Hence, we propose a framework, ADFlow, to monitor and adapt the workflow of the Web service composition when necessary to maximize its ability to satisfy the non-functional requirements automatically. To reduce the monitoring overhead, ADFlow relies on asynchronous monitoring. ADFlow has been implemented and …

Scaling Bdd-Based Timed Verification With Simulation Reduction, Truong Khanh Nguyen, Tian Huat Tan, Jun Sun, Jiaying Li, Yang Liu, Manman Chen, Jin Song Dong

Research Collection School Of Computing and Information Systems

Digitization is a technique that has been widely used in real-time model checking. With the assumption of digital clocks, symbolic model checking techniques (like those based on BDDs) can be applied for real-time systems. The problem of model checking real-time systems based on digitization is that the number of tick transitions increases rapidly with the increment of clock upper bounds. In this paper, we propose to improve BDD-based verification for real-time systems using simulation reduction. We show that simulation reduction allows us to verify timed automata with large clock upper bounds and to converge faster to the fixpoint. The presented …

Designing And Evaluating Business Process Models: An Experimental Approach, Yuecheng Martin Yu, Alexander Pelaez, Karl R. Lang

Research Collection School Of Computing and Information Systems

This paper presents an experimental approach to compare the performance of alternative business process designs. We use an example case of an electronic group buying setting to demonstrate how our approach can be applied in practice. More specifically, we chose a standard business process, the sales process as implemented on a group buying platform, to illustrate how a business process may be redesigned in order to better meet the needs of customers. For that purpose, we introduce a social technology feature to support cooperation among buyers in the sales process and then analyze the performance impact of the proposed business …

A Parallel 3d Phase-Field Simulation Of Multi-Grain Growth Based On The Full Thread Tree, Ya-Jun Yin, Min Wang, Jian-Xin Zhou, Dun-Ming Liao, Xu Shen, Tao Chen

The 8th International Conference on Physical and Numerical Simulation of Materials Processing

No abstract provided.

Techniques For Identifying Mobile Platform Vulnerabilities And Detecting Policy-Violating Applications, Mon Kywe Su

Dissertations and Theses Collection

Mobile systems are generally composed of three layers of software: application layer where third-party applications are installed, framework layer where Application Programming Interfaces (APIs) are exposed, and kernel layer where low-level system operations are executed. In this dissertation, we focus on security and vulnerability analysis of framework and application layers. Security mechanisms, such as Android’s sandbox and permission systems, exist in framework layer, while malware scanners protects application layer. However, there are rooms for improvement in both mechanisms. For instance, Android’s permission system is known to be implemented in ad-hoc manner and not well-tested for vulnerabilities. Application layer also focuses …

Pattern Synonyms, Matthew Pickering, Gergő Érdi, Simon Peyton Jones, Richard A. Eisenberg

Computer Science Faculty Research and Scholarship

Pattern matching has proven to be a convenient, expressive way of inspecting data. Yet this language feature, in its traditional form, is limited: patterns must be data constructors of concrete data types. No computation or abstraction is allowed. The data type in question must be concrete, with no ability to enforce any invariants. Any change in this data type requires all clients to update their code.

This paper introduces pattern synonyms, which allow programmers to abstract over patterns, painting over all the shortcomings listed above. Pattern synonyms are assigned types, enabling a compiler to check the validity of a …

On The Feasibility Of Detecting Cross-Platform Code Clones Via Identifier Similarity, Xiao Cheng, Lingxiao Jiang, Hao Zhong, Haibo Yu, Jianjun Zhao

Research Collection School Of Computing and Information Systems

More and more mobile applications run on multiple mobile operating systems to attract more users of different platforms. Although versions on different platforms are implemented in different programming languages (e.g., Java and Objective-C), there must be many code snippets that implement the similar business logic on different platforms. Such code snippets are called cross-platform clones. It is challenging but essential to detect such clones for software maintenance. Due to the practice that developers usually use some common identifiers when implementing the same business logic on different platforms, in this paper, we investigate the identifier similarity of the same mobile application …

Mining Revision Histories To Detect Cross-Language Clones Without Intermediates, Lingxiao Jiang, Zhiming Peng, Lingxiao Jiang, Hao Zhong, Haibo Yu, Jianjun Zhao

Research Collection School Of Computing and Information Systems

To attract more users on different platforms, many projects release their versions in multiple programming languages (e.g., Java and C#). They typically have many code snippets that implement similar functionalities, i.e., cross-language clones. Programmers often need to track and modify cross-language clones consistently to maintain similar functionalities across different language implementations. In literature, researchers have proposed approaches to detect cross-language clones, mostly for languages that share a common intermediate language (such as the .NET language family) so that techniques for detecting single-language clones can be applied. As a result, those approaches cannot detect cross-language clones for many projects that are …

Effective Compiler Error Message Enhancement For Novice Programming Students, Brett Becker Dr, Graham Glanville

Faculty Research

Programming is an essential skill that all computing students must master. However programming can be difficult to learn. Compiler error messages are crucial for correcting errors, but are often difficult to understand and pose a barrier to progress for many novices. High frequencies of errors, particularly repeated errors, have been shown to be indicators of students who are struggling with learning to program. This study involves a custom IDE that enhances Java compiler error messages, intended to be more useful to novices than those supplied by the compiler. The effectiveness of this approach was tested in an empirical control/intervention study …

Decision Modeling And Empirical Analysis Of Mobile Financial Services, Jun Liu

Dissertations and Theses Collection

The past twenty years have been a time of many new technological developments, changing business practices, and interesting innovations in the financial information system (IS) and technology landscape. As the financial services industry has been undergoing the digital transformation, the emergence of mobile financial services has been changing the way that customers pay for goods and services purchases and interact with financial institutions. This dissertation seeks to understand the evolution of the mobile payments technology ecosystem and how firms make mobile payments investment decisions under uncertainty, as well as examines the influence of mobile banking on customer behavior and financial …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.3.1 patched

CHANGES IN R 3.3.1

CHANGES IN R 3.3.0

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

In the past 8 months,1322 new packages were added to the CRAN package repository. 43 packages were unarchived,48 archived,1 package had to be removed.The following shows the growth of the number of active packages in the CRAN package repository:

Nonparametric Tests For The Interaction In Two-Way Factorial Designs Using R, Jos Feys

The R Journal

An increasing number of R packages include nonparametric tests for the interaction in two-way factorial designs. This paper briefly describes the different methods of testing and reports the resulting p-values of such tests on datasets for four types of designs: between, within, mixed, and pretest-posttest designs. Potential users are advised only to apply tests they are quite familiar with and not be guided by p-values for selecting packages and tests.

Using Decipher V2.0 To Analyze Big Biological Sequence Data In R, Erik S. Wright

The R Journal

In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biological sequences. This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time. It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects. The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in …

Scmamp: Statistical Comparison Of Multiple Algorithms In Multiple Problems, Borja Calvo, Guzmán Santafé

The R Journal

Comparing the results obtained by two or more algorithms in a set of problems is a central task in areas such as machine learning or optimization. Drawing conclusions from these comparisons may require the use of statistical tools such as hypothesis testing. There are some interesting papers that cover this topic. In this manuscript we present scmamp, an R package aimed at being a tool that simplifies the whole process of analyzing the results obtained when comparing algorithms, from loading the data to the production of plots and tables.

Comparing the performance of different algorithms is an essential step …

Swmpr: An R Package For Retrieving, Organizing, And Analyzing Environmental Data For Estuaries, Marcus W. Beck

The R Journal

The System-Wide Monitoring Program (SWMP)was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, and analysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to …

Spatio-Temporal Interpolation Using Gstat, Benedikt Gräler, Edzer Pebesma, Gerard Heuvelink

The R Journal

We present new spatio-temporal geostatistical modelling and interpolation capabilities of the R package gstat. Various spatio-temporal covariance models have been implemented, such as the separable, product-sum, metric and sum-metric models. Inareal-world application we comparespatio temporal interpolations using these models with a purely spatial kriging approach. The target variable of the application is the daily mean PM10 concentration measured at rural air quality monitoring stations across Germany in 2005. R code for variogram fitting and interpolation is presented in this paper to illustrate the workflow of spatio-temporal interpolation using gstat. We conclude that the system works properly and that the …

Model Builder For Item Factor Analysis With Openmx, Joshua N. Pritikin, Karen M. Schmidt

The R Journal

We introduce a shiny web application to facilitate the construction of Item Factor Analysis (a.k.a. Item Response Theory) models using the OpenMx package. The web application assists with importing data, outcome recoding, and model specification. However, the app does not conduct any analysis but, rather, generates an analysis script. Generated Rmarkdown output serves dual purposes: to analyze a data set and demonstrate good programming practices. The app can be used as a teaching tool or as a starting point for custom analysis scripts.