Programming Languages and Compilers Commons^™

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 …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. Bioconductor 3.4 was released on 18 October, 2016. It is com patible with R 3.3 and consists of 1296 software packages, 309 experiment data packages, and 933 up-to-date annotation packages. The release announcement includes descriptions of 101 new packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

Weighted Distance Based Discriminant Analysis: The R Package Wedibadis, Itziar Irigoien, Francesc Mestres, Concepcion Arenas

The R Journal

The WeDiBaDis package provides a user friendly environment to perform discriminant analysis (supervised classification). WeDiBaDis is an easy to use package addressed to the biological and medical communities, and in general, to researchers interested in applied studies. It can be suitable when the user is interested in the problem of constructing a discriminant rule on the basis of distances between a relatively small number of instances or units of known unbalanced-class membership measured on many (possibly thousands) features of any type. This is a current situation when analyzing genetic biomedical data. This discriminant rule can then be used both, as …

Computing Pareto Frontiers And Database Preferences With The Rpref Package, Patrick Roocks

The R Journal

The concept of Pareto frontiers is well-known in economics. Within the database community there exist many different solutions for the specification and calculation of Pareto frontiers, also called Skyline queries in the database context. Slight generalizations like the combination of the Pareto operator with the lexicographical order have been established under the term database preferences. In this paper we present the rPref package which allows to efficiently deal with these concepts within R. With its help, database preferences can be specified in a very similar way as in a state-of-the-art database management system. Our package provides algorithms for an …

Dcovts: Distance Covariance/Correlation For Time Series, Maria Pitsillou, Konstantinos Fokianos

The R Journal

The distance covariance function is a new measure of dependence between random vectors. We drop the assumption of iid data to introduce distance covariance for time series. The R package dCovTS provides functions that compute and plot distance covariance and correlation functions for both univariate and multivariate time series. Additionally it includes functions for testing serial independence based on distance covariance. This paper describes the theoretical background of distance covariance methodology in time series and discusses in detail the implementation of these methods with the R package dCovTS.

Escape From Boxland, Barret Schloerke, Hadley Wickham, Dianne Cook, Heike Hofmann

The R Journal

A library of common geometric shapes can be used to train our brains for understanding data structure in high-dimensional Euclidean space. This article describes the methods for producing cubes, spheres, simplexes, and tori in multiple dimensions. It also describes new ways to define and generate high-dimensional tori. The algorithms are described, critical code chunks are given, and a large collection of generated data are provided. These are available in the R package geozoo, and selected movies and images, are available on the GeoZoo web site (http://schloerke.github.io/geozoo/)

An Introduction To Principal Surrogate Evaluation With The Pseval Package, Michael C. Sachs, Erin E. Gabriel

The R Journal

We describe a new package called pseval that implements the core methods for the evaluation of principal surrogates in a single clinical trial. It provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation methods are provided, including print, summary, plot, and testing. We summarize the main statistical methods that are implemented in the package and illustrate its use from the perspective …

Variants Of Simple Correspondence Analysis, Rosaria Lombardo, Eric J. Beh

The R Journal

This paper presents the R package CAvariants (Lombardo and Beh, 2017). The package performs six variants of correspondence analysis on a two-way contingency table. The main function that shares the same name as the package– CAvariants– allows the user to choose (via a series of input parameters) from six different correspondence analysis procedures. These include the classical approach to (symmetrical) correspondence analysis, singly ordered correspondence analysis, doubly ordered correspondence analysis, non symmetrical correspondence analysis, singly ordered non symmetrical correspondence analysis and doubly ordered non symmetrical correspondence analysis. The code provides the flexibility for constructing either a classical correspondence plot or …

Design Of The Tronco Bioconductor Package For Translational Oncology, Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti

The R Journal

Models of cancer progression provide insights on the order of accumulation of genetic alterations during cancer development. Algorithms to infer such models from the currently available mutational profiles collected from different cancer patients (cross-sectional data) have been defined in the literature since late the 90s. These algorithms differ in the way they extract a graphical model of the events modelling the progression, e.g., somatic mutations or copy-number alterations.

TRONCO is an R package for TRanslational ONcology which provides a series of functions to assist the user in the analysis of cross-sectional genomic data and, in particular, it implements …

Multiplencc: Inverse Probability Weighting Of Nested Case-Control Data, Nathalie C. Støer, Sven Ove Samuelsen

The R Journal

Reuse of controls from nested case-control designs can increase efficiency in many situations, for instance with competing risks or in other multiple endpoints situations. The matching between cases and controls must be broken when controls are to be used for other endpoints. A weighted analysis can then be performed to take care of the biased sampling from the cohort. We present the R package multipleNCC for reuse of controls in nested case-control studies by inverse probability weighting of the partial likelihood. The package handles right-censored, left-truncated and additionally matched data, and varying numbers of sampled controls and the whole analysis …

Editorial, Michael Lawrence

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 8, Issue 2 of the R Journal. This issue contains 33 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). This issue highlights the breadth and depth of the R package ecosystem, covering advances in statistical computing and visualization, as well as novel applications of R in specific domains. The authors have described a small but representative sample of the now more than 11000 packages …

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 …

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 …

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 …

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 …