Programming Languages and Compilers Commons^™

Editorial, Bettina Grün

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 7, Issue 2 of the R Journal. This issue contains 20 contributed research articles and several contributions to the News and Notes section.

Code Profiling In R: A Review Of Existing Methods And An Introduction To Package Guiprofiler, Angel Rubio, Fernando De Villar

The R Journal

Code analysis tools are crucial to understand program behavior. Profile tools use the results of time measurements in the execution of a program to gain this understanding and thus help in the optimization of the code. In this paper, we review the different available packages to profile R code and show the advantages and disadvantages of each of them. In additon, we present GUIProfiler, a package that fulfills some unmet needs

Package GUIProfiler generates an HTML report with the timing for each code line and the relationships between different functions. This package mimics the behavior of the MATLAB profiler. …

Quantifquantile: An R Package For Performing Quantile Regression Through Optimal Quantization, Isabelle Charlier, Davy Paindaveine, Jérôme Saracco

The R Journal

In quantile regression, various quantiles of a response variable Y are modelled as functions of covariates (rather than its mean). An important application is the construction of reference curves/surfaces and conditional prediction intervals for Y. Recently, a nonparametric quantile regression method based on the concept of optimal quantization was proposed. This method competes very well with k-nearest neighbor, kernel, and spline methods. In this paper, we describe an R package, called QuantifQuantile, that allows to perform quantization-based quantile regression. We describe the various functions of the package and provide examples.

Changes In R, The R Core Team

The R Journal

CHANGES IN R 3.2.3

CHANGES IN R 3.2.2

The R Consortium And The R Foundation, Martyn Plummer

The R Journal

The R Consortium was announced at the useR! 2015 conference in Aalborg, Denmark on 30 June. It is a non-profit organization set up to provide infrastructure for the R community. The purpose of this article is to explain some of the background to the setting up of the Consortium and how it interacts with the R Foundation.

An Immersive Telepresence System Using Rgb-D Sensors And Head-Mounted Display, Xinzhong Lu, Ju Shen, Saverio Perugini, Jianjun Yang

Computer Science Faculty Publications

We present a tele-immersive system that enables people to interact with each other in a virtual world using body gestures in addition to verbal communication. Beyond the obvious applications, including general online conversations and gaming, we hypothesize that our proposed system would be particularly beneficial to education by offering rich visual contents and interactivity. One distinct feature is the integration of egocentric pose recognition that allows participants to use their gestures to demonstrate and manipulate virtual objects simultaneously. This functionality enables the instructor to effectively and efficiently explain and illustrate complex concepts or sophisticated problems in an intuitive manner. The …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

News From The Bioconductor Project, The Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1104 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/. Navigate packages using ‘biocViews’ terms and title search. Each package has an html page with a description, links to vignettes, reference manuals, and usage statistics. Start using Bioconductor version 3.2 by installing R 3.2.3 and evaluating the commands

The R Journal (December 2015) 7(2): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Fitting Conditional and Simultaneous Autoregressive Spatial Models in hglm, Moudud Alam, Lars Rönnegård, and Xia Shen

VSURF: An R Package for Variable Selection Using Random Forests, Robin Genuer, Jean-Michel Poggi, and Christine Tuleau-Malot

zoib: An R Package for Bayesian Inference for Beta Regression and Zero/One Inflated Beta Regression, Fang Liu, and Yunchuan Kong

apc: An R Package for Age-Period-Cohort Analysis, Bent Nielsen

QuantifQuantile: An R Package for Performing Quantile Regression Through Optimal Quantization, Isabelle Charlier, Davy Paindaveine, and Jérôme Saracco

Numerical Evaluation of the Gauss Hypergeometric Function with the hypergeo Package, Robin K. S. …

Open-Channel Computation With R, Michael C. Koohafkan, Bassam A. Younis

The R Journal

The rivr package provides a computational toolset for simulating steady and unsteady one dimensional flows in open channels. It is designed primarily for use by instructors of undergraduate and graduate-level open-channel hydrodynamics courses in such diverse fields as river engineering, physical geography and geophysics. The governing equations used to describe open-channel flows are briefly presented, followed by example applications. These include the computation of gradually varied flows and two examples of unsteady flows in channels—namely, the tracking of the evolution of a flood wave in a channel and the prediction of extreme variation in the water-surface profile that results when …

Mtk: A General-Purpose And Extensible R Environment For Uncertainty And Sensitivity Analyses Of Numerical Experiments, Juhui Wang, Robert Faivre, Hervé Richard, Hervé Monod

The R Journal

Along with increased complexity of the models used for scientific activities and engineering come diverse and greater uncertainties. Today, effectively quantifying the uncertainties contained in a model appears to be more important than ever. Scientific fellows know how serious it is to calibrate their model in a robust way, and decision-makers describe how critical it is to keep the best effort to reduce the uncertainties about the model. Effectively accessing the uncertainties about the model requires mastering all the tasks involved in the numerical experiments, from optimizing the experimental design to managing the very time consuming aspect of model simulation …

Altopt: An R Package For Optimal Experimental Design Of Accelerated Life Testing, Kangwon Seo, Rong Pan

The R Journal

The R package ALTopt has been developed with the aim of creating and evaluating optimal experimental designs of censored accelerated life tests (ALTs). This package takes the generalized linear model approach to ALT planning, because this approach can easily handle censoring plans and derive information matrices for evaluating designs. Three types of optimality criteria are considered: D-optimality for model parameter estimation, U-optimality for reliability prediction at a single use condition, and I-optimality for reliability prediction over a region of use conditions. The Weibull distribution is assumed for failure time data and more than one stress factor can …

Working With Multilabel Datasets In R: The Mldr Package, Francisco Charte, David Charte

The R Journal

Most classification algorithms deal with datasets which have a set of input features, the variables to be used as predictors, and only one output class, the variable to be predicted. However, in late years many scenarios in which the classifier has to work with several outputs have come to life. Automatic labeling of text documents, image annotation or protein classification are among them. Multilabel datasets are the product of these new needs, and they have many specific traits. The mldr package allows the user to load datasets of this kind, obtain their characteristics, produce specialized plots, and manipulate them. The …

Bsgs: Bayesian Sparse Group Selection, Kuo-Jung Lee, Ray-Bing Chen

The R Journal

An R package BSGS is provided for the integration of Bayesian variable and sparse group selection separately proposed by Chen et al. (2011) and Chen et al. (in press) for variable selection problems, even in the cases of large p and small n. This package is designed for variable selection problems including the identification of the important groups of variables and the active variables within the important groups. This article introduces the functions in the BSGS package that can be used to perform sparse group selection as well as variable selection through simulation studies and real data.

Apc: An R Package For Age-Period-Cohort Analysis, Bent Nielsen

The R Journal

The apc package includes functions for age-period-cohort analysis based on the canonical parametrisation of Kuang et al. (2008a). The package includes functions for organizing the data, descriptive plots, a deviance table, estimation of (sub-models of) the age-period-cohort model, a plot for specification testing, plots of estimated parameters, and sub-sample analysis.

Fitting Conditional And Simultaneous Autoregressive Spatial Models In Hglm, Moudud Alam, Lars Rönnegård, Xia Shen

The R Journal

We present a new version ( 2.0) of the hglm package for fitting hierarchical generalized linear models (HGLMs) with spatially correlated random effects. CAR() and SAR() families for con ditional and simultaneous autoregressive random effects were implemented. Eigen decomposition of the matrix describing the spatial structure (e.g., the neighborhood matrix) was used to transform the CAR/SARrandomeffects into an independent, but heteroscedastic, Gaussian random effect. A linear predictor is fitted for the random effect variance to estimate the parameters in the CAR and SAR models. This gives a computationally efficient algorithm for moderately sized problems.

Transforming C Openmp Programs For Verification In Civl, Michael Rogers

School of Computing: Dissertations, Theses, and Student Research

There are numerous way to express parallelism which can make it challenging for developers to verify these programs. Many tools only target a single dialect but the Concurrency Intermediate Verification Language (CIVL) targets MPI, Pthreads, and CUDA. CIVL provides a general concurrency model that can represent pro- grams in a variety of concurrency dialects. CIVL includes a front-end that support all of the dialects mentioned above. The back-end is a verifier that uses model checking and symbolic execution to check standard properties.

In this thesis, we have designed and implemented a transformer that will take C OpenMP programs and transform …

Challenges In Analyzing Software Documentation In Portuguese, Christoph Treude, Carlos A. Prolo, Fernando Figueira Filho

Research Collection School Of Computing and Information Systems

Many tools that automatically analyze, summarize, or transform software artifacts rely on natural language processing tooling for the interpretation of natural language text produced by software developers, such as documentation, code comments, commit messages, or bug reports. Processing natural language text produced by software developers is challenging because of unique characteristics not found in other texts, such as the presence of code terms and the systematic use of incomplete sentences. In addition, texts produced by Portuguese-speaking developers mix languages since many keywords and programming concepts are referred to by their English name. In this paper, we provide empirical insights into …

Codehow: Effective Code Search Based On Api Understanding And Extended Boolean Model (E), Fei Lv, Jian-Guang Lou, Shaowei Wang, Dongmei Zhang, Jainjun Zhao

Research Collection School Of Computing and Information Systems

Over the years of software development, a vast amount of source code has been accumulated. Many code search tools were proposed to help programmers reuse previously-written code by performing free-text queries over a large-scale codebase. Our experience shows that the accuracy of these code search tools are often unsatisfactory. One major reason is that existing tools lack of query understanding ability. In this paper, we propose CodeHow, a code search technique that can recognize potential APIs a user query refers to. Having understood the potentially relevant APIs, CodeHow expands the query with the APIs and performs code retrieval by applying …

Detecting Broken Pointcuts Using Structural Commonality And Degree Of Interest, Raffi Khatchadourian, Awais Rashd, Hidehiko Masuhara, Takuya Watanabe

Publications and Research

Pointcut fragility is a well-documented problem in Aspect-Oriented Programming; changes to the base code can lead to join points incorrectly falling in or out of the scope of pointcuts. Deciding which pointcuts have broken due to base-code changes is daunting, especially in large and complex systems. We present an automated approach that recommends pointcuts that are likely to require modification due to a certain base-code change and ones that do not. Our hypothesis is that join points selected by a pointcut exhibit common structural characteristics. Patterns describing such commonalities recommend pointcuts that have potentially broken to the developer. The approach …