Numerical Analysis and Scientific Computing Commons^™

The Stringdist Package For Approximate String Matching, Mark P.J. Van Der Loo

The R Journal

Comparing text strings in terms of distance functions is a common and fundamental task in many statistical text-processing applications. Thus far, string distance functionality has been somewhat scattered around R and its extension packages, leaving users with inconistent interfaces and encoding handling. The stringdist package was designed to offer a low-level interface to several popular string distance algorithms which have been re-implemented in C for this purpose. The package offers distances based on counting q-grams, edit-based distances, and some lesser known heuristic distance functions. Based on this functionality, the package also offers inexact matching equivalents of R’s native exact matching …

Sgr: A Package For Simulating Conditional Fake Ordinal Data, Luigi Lombardi, Massimiliano Pastore

The R Journal

Many self-report measures of attitudes, beliefs, personality, and pathology include items that can be easily manipulated by respondents. For example, an individual may deliberately attempt to manipulate or distort responses to simulate grossly exaggerated physical or psychological symptoms in order to reach specific goals such as, for example, obtaining financial compensation, avoiding being charged with a crime, avoiding military duty, or obtaining drugs. This article introduces the package sgr that can be used to perform fake data analysis according to the sample generation by replacement approach. The package includes functions for making simple inferences about discrete/ordinal fake data. The package …

The Gridsvg Package, Paul Murrell, Simon Potter

The R Journal

The gridSVG package can be used to generate a grid-based R plot in an SVG format, with the ability to add special effects to the plot. The special effects include animation, interactivity, and advanced graphical features, such as masks and filters. This article provides a basic introduction to important functions in the gridSVG package and discusses the advantages and disadvantages of gridSVG compared to similar R packages.

News From The Bioconductor Project, Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 824 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/release/. 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 and R version 3.1.0 with

Rstorm: Developing And Testing Streaming Algorithms In R, Maurits Kaptein

The R Journal

Streaming data, consisting of indefinitely evolving sequences, are becoming ubiquitous in many branches of science and in various applications. Computer scientists have developed streaming applications such as Storm and the S4 distributed stream computing platform1 to deal with data streams. However, in current production packages testing and evaluating streaming algorithms is cumbersome. This paper presents RStorm for the development and evaluation of streaming algorithms analogous to these production packages, but implemented fully in R. RStorm allows developers of streaming algorithms to quickly test, iterate, and evaluate various implementations of streaming algorithms. The paper provides both a canonical computer science example, …

A Multiscale Test Of Spatial Stationarity For Textured Images In R, Matthew A. Nunes, Sarah L. Taylor, Idris A. Eckley

The R Journal

The ability to automatically identify areas of homogeneous texture present within a greyscale image is an important feature of image processing algorithms. This article describes the R package LS2W stat which employs a recent wavelet-based test of stationarity for locally stationary random fields to assess such spatial homogeneity. By embedding this test within a quadtree image segmentation procedure we are also able to identify texture regions within an image.

Editorial, Deepayan Sarkar

The R Journal

Onbehalf of the editorial board, I am pleased to publish Volume 6, Issue 1 of the R Journal.

Rankcluster: An R Package For Clustering Multivariate Partial Rankings, Julien Jacques, Quentin Grimonprez, Christophe Biernacki

The R Journal

The Rankcluster package is the first R package proposing both modeling and clustering tools for ranking data, potentially multivariate and partial. Ranking data are modeled by the Insertion Sorting Rank (ISR) model, which is a meaningful model parametrized by a central ranking and a dispersion parameter. A conditional independence assumption allows multivariate rankings to be taken into account, and clustering is performed by means of mixtures of multivariate ISR models. The parameters of the cluster (central rankings and dispersion parameters) help the practitioners to interpret the clustering. Moreover, the Rankcluster package provides an estimate of the missing ranking positions when …

Addendum To “Statistical Software From A Blind Person's Perspective'”, A. Johnathan, R. Godfrey, Robert Erhardt

The R Journal

This short note explains a solution to a problem for blind users when using the R terminal under Windows Vista or Windows 7, as identified in Godfrey (2013). We note the way the solution was discovered and subsequent confirmatory experiments.

Pivotalr: A Package For Machine Learning On Big Data, Hai Qian

The R Journal

PivotalR is an R package that provides a front-end to PostgreSQL and all PostgreSQL like databases such as Pivotal Inc.’s Greenplum Database (GPDB), HAWQ. When running on the products of Pivotal Inc., PivotalR utilizes the full power of parallel computation and distributive storage, and thus gives the normal R user access to big data. PivotalR also provides an R wrapper for MADlib. MADlib is an open-source library for scalable in-database analytics. It provides data-parallel implementations of mathematical, statistical and machine-learning algorithms for structured and unstructured data. Thus PivotalR also enables the user to apply machine learning algorithms on big data.

Rose: A Package For Binary Imbalanced Learning, Nicola Lunardon, Giovanna Menardi, Nicola Torelli

The R Journal

The ROSE package provides functions to deal with binary classification problems in the presence of imbalanced classes. Artificial balanced samples are generated according to a smoothed bootstrap approach and allow for aiding both the phases of estimation and accuracy evaluation of a binary classifier in the presence of a rare class. Functions that implement more traditional remedies for the class imbalance and different metrics to evaluate accuracy are also provided. These are estimated by holdout, bootstrap, or cross-validation methods.

Stratified Weibull Regression Model For Interval-Censored Data, Xiangdong Gu, David Shapiro, Michael D. Hughes, Raji Balasubramanian

The R Journal

Interval censored outcomes arise when a silent event of interest is known to have occurred within a specific time period determined by the times of the last negative and first positive diagnostic tests. There is a rich literature on parametric and non-parametric approaches for the analysis of interval-censored outcomes. A commonly used strategy is to use a proportional hazards (PH) model with the baseline hazard function parameterized. The proportional hazards assumption can be relaxed in stratified models by allowing the baseline hazard function to vary across strata defined by a subset of explanatory variables. In this paper, we describe and …

Mrcv: A Package For Analyzing Categorical Variables With Multiple Response Options, Natalie A. Koziol, Christopher R. Bilder

The R Journal

Multiple response categorical variables (MRCVs), also known as “pick any” or “choose all that apply” variables, summarize survey questions for which respondents are allowed to select more than one category response option. Traditional methods for analyzing the association between categorical variables are not appropriate with MRCVs due to the within-subject dependence among responses. We have developed the MRCV package as the first R package available to correctly analyze MRCVdata. Statistical methods offered by our package include counterparts to traditional Pearson chi-square tests for independence and loglinear models, where bootstrap methods and Rao-Scott adjustments are relied on to obtain valid inferences. …

Changes In R, The R Core Team

The R Journal

CHANGES IN R 3.1.1

CHANGES IN R 3.1.0

CHANGES IN R 3.0.3

The Rwiener Package: An R Package Providing Distribution Functions For The Wiener Diffusion Model, Dominik Wabersich, Joachim Vandekerckhove

The R Journal

We present the RWiener package that provides R functions for the Wiener diffusion model. The core of the package are the four distribution functions dwiener, pwiener, qwiener and rwiener, which use up-to-date methods, implemented in C, and provide fast and accurate computation of the density, distribution, and quantile function, as well as a random number generator for the Wiener diffusion model. We used the typical Wiener diffusion model with four parameters: boundary separation, non-decision time, initial bias and drift rate parameter. Beyond the distribution functions, weprovide extended likelihood-based functions that can be used for parameter estimation and model selection. The …

Fully Differential Cross Sections For Electron-Impact Excitation-Ionization Of Aligned D₂, Esam Ali, A. L. Harris, J. Lower, E. Weigold, Chuang-Gang Ning, Don H. Madison

Physics Faculty Research & Creative Works

We examine fully differential cross sections for 176 eV electron-impact dissociative excitation-ionization of orientated D2 for transitions to final ion states 2sσ_g, 2pσ_u, and 2pπ_u. In previous work [Phys. Rev. A 88, 062705 (2013)PLRAAN1050-294710.1103/PhysRevA.88.062705], we calculated these cross sections using the molecular four-body distorted wave (M4DW) method with the ground-state D2 wave function being approximated by a product of two Dyson 1s-type orbitals. The theoretical results were compared with experimental measurements for five different orientations of the target molecule (four in the scattering plane and one perpendicular to the scattering plane). For the unresolved …

Theoretical Triple-Differential Cross Sections Of A Methane Molecule By A Proper-Average Method, Hari Chaluvadi, C. G. Ning, Don H. Madison

Physics Faculty Research & Creative Works

For the last few years, our group has calculated cross sections for electron-impact ionization of molecules using the molecular three-body distorted-wave approximation coupled with the orientation-averaged molecular orbital (OAMO) approximation. This approximation was very successful for calculating ionization cross sections for hydrogen molecules and to a lesser extent nitrogen molecules. Recently we used the approximation to calculate single ionization cross sections for the 1t₂ state of methane (CH₄) and we found major discrepancies with the experimental data. Here we investigate the validity of the OAMO approximation by calculating cross sections that have been properly averaged over all …

Graph-Based Semi-Supervised Learning: Realizing Pointwise Smoothness Probabilistically, Yuan Fang, Kevin Chen-Chuan Chang, Hady W. Lauw

Research Collection School Of Computing and Information Systems

As the central notion in semi-supervised learning, smoothness is often realized on a graph representation of the data. In this paper, we study two complementary dimensions of smoothness: its pointwise nature and probabilistic modeling. While no existing graph-based work exploits them in conjunction, we encompass both in a novel framework of Probabilistic Graph-based Pointwise Smoothness (PGP), building upon two foundational models of data closeness and label coupling. This new form of smoothness axiomatizes a set of probability constraints, which ultimately enables class prediction. Theoretically, we provide an error and robustness analysis of PGP. Empirically, we conduct extensive experiments to show …

Ar-Miner: Mining Informative Reviews For Developers From Mobile App Marketplace, Ning Chen, Jialiu Lin, Steven C. H. Hoi, Xiaokui Xiao, Boshen Zhang

Research Collection School Of Computing and Information Systems

With the popularity of smartphones and mobile devices, mobile application (a.k.a. “app”) markets have been growing exponentially in terms of number of users and downloads. App developers spend considerable effort on collecting and exploiting user feedback to improve user satisfaction, but suffer from the absence of effective user review analytics tools. To facilitate mobile app developers discover the most “informative” user reviews from a large and rapidly increasing pool of user reviews, we present “AR-Miner” — a novel computational framework for App Review Mining, which performs comprehensive analytics from raw user reviews by (i) first extracting informative user reviews by …

On Efficient Reverse Skyline Query Processing, Yunjun Gao, Qing Liu, Baihua Zheng, Gang Chen

Research Collection School Of Computing and Information Systems

Given a D-dimensional data set P and a query point q, a reverse skyline query (RSQ) returns all the data objects in P whose dynamic skyline contains q. It is important for many real life applications such as business planning and environmental monitoring. Currently, the state-of-the-art algorithm for answering the RSQ is the reverse skyline using skyline approximations (RSSA) algorithm, which is based on the precomputed approximations of the skylines. Although RSSA has some desirable features, e.g., applicability to arbitrary data distributions and dimensions, it needs for multiple accesses of the same nodes, incurring redundant I/O and CPU costs. In …

Air Indexing For On-Demand Xml Data Broadcast, Weiwei Sun, Rongrui Qin, Jinjin Wu, Baihua Zheng

Research Collection School Of Computing and Information Systems

XML data broadcast is an efficient way to disseminate semi-structured information in wireless mobile environments. In this paper, we propose a novel two-tier index structure to facilitate the access of XML document in an on-demand broadcast system. It provides the clients with an overall image of all the XML documents available at the server side and hence enables the clients to locate complete result sets accordingly. A pruning strategy is developed to cut down the index size and a two-tier structure is proposed to further remove any redundant information. In addition, two index distribution strategies, namely naive distribution and partial …

Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum, Tao Zeng

Computer Science Theses & Dissertations

One significant difference between evolved mammalian brains and other species is that mammalian brains exhibit increasingly convoluted structures in the cerebral cortex. Groove and ridge shaped structures named gyri and sulci expand surface area of cerebral cortex, making more functions possible. Prior studies using neuroimaging techniques such as dMRI and DTI have revealed that neural fibers are heavily connected to gyri comparing to those connected to sulci, such macro-scale experiments indicates that gyri are involved in large scale information processing while sulci process information locally. However, molecular and cellar level evidences, namely, gene expression pattern and its resulting neuronal connectivity …

Hydrographic Surface Modeling Through A Raster Based Spline Creation Method, Julie G. Alexander

LSU New Orleans Theses and Dissertations

The United States Army Corp of Engineers relies on accurate and detailed surface models for various construction projects and preventative measures. To aid in these efforts, it is necessary to work for advancements in surface model creation. Current methods for model creation include Delaunay triangulation, raster grid interpolation, and Hydraulic Spline grid generation. While these methods produce adequate surface models, attempts for improved methods can still be made.

A method for raster based spline creation is presented as a variation of the Hydraulic Spline algorithm. By implementing Hydraulic Splines in raster data instead of vector data, the model creation process …

A Uniform Database Of Teleseismic Shear Wave Splitting Measurements For The Western And Central United States, Kelly H. Liu, Ahmed Elsheikh, Awas Lemnifi, Uranbaigal Purevsuren, Melissa Ray, Hesham Refayee, Bin B. Yang, Youqiang Yu, Stephen S. Gao

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

We present a shear wave splitting (SWS) database for the western and central United States as part of a lasting effort to build a uniform SWS database for the entire North America. The SWS measurements were obtained by minimizing the energy on the transverse component of the PKS, SKKS, and SKS phases. Each of the individual measurements was visually checked to ensure quality. This version of the database contains 16,105 pairs of splitting parameters. The data used to generate the parameters were recorded by 1774 digital broadband seismic stations over the period of 1989-2012, and represented all the available data …

Canaries In The Urban Data Mine: Analytics For Smarter City Life, Robert J. Kauffman

Research Collection School Of Computing and Information Systems

Technology-based sensors and data analytics have created unprecendented levels of informedness for consumers, corporations, the public and government agencies. The information they generated provides a basis for smarter cities and more sustainable urban living.

How Many Eyeballs Does A Bug Need? An Empirical Validation Of Linus' Law, Subhajit Datta, Proshanta Sarkar, Sutirtha Das, Sonu Sreshtha, Prasanth Lade, Subhashis Majumder

Research Collection School Of Computing and Information Systems

Linus’ Law reflects on a key characteristic of open source software development: developers’ tendency to closely work together in the bug resolution process. In this paper we empirically examine Linus’ Law using a data-set of 1,000+ Android bugs, owned by 70+ developers. Our results indicate that encouraging developers to work closely with one another has nuanced implications; while one form of contact may help reduce bug resolution time, another form can have quite the opposite effect. We present statistically significant evidence in support of our results and discuss their relevance at the individual and organizational levels.

Generating Combinatorial Objects- A New Perspective, Alexander Chizoma Nwala

Computer Science Theses & Dissertations

Combinatorics is the science of "possibilities." This definition, while not formal is a fair statement because all too often, in order to gain insight into the solution of many counting problems, we explore the possibilities. In some cases we seek to know how many options, while in other cases we seek to enumerate or list the options. Irrespective of the scenario, combinatorics plays a vital role today. In many instances such as exploring the options for choosing a new password for a combination lock, we employ combinatorics. In considering the possible license plate permutations for a state, or to see …

New Pod Error Expressions, Error Bounds, And Asymptotic Results For Reduced Order Model Of Parabolic Pdes, John R. Singler

Mathematics and Statistics Faculty Research & Creative Works

The derivations of existing error bounds for reduced order models of time varying partialdi erential equations (PDEs) constructed using proper orthogonal decomposition (POD) haverelied on bounding the error between the POD data and various POD projections of that data.Furthermore, the asymptotic behavior of the model reduction error bounds depends on theasymptotic behavior of the POD data approximation error bounds. We consider time varyingdata taking values in two di erent Hilbert spacesHandV, withVH, and prove exactexpressions for the POD data approximation errors considering four di erent POD projectionsand the two di erent Hilbert space error norms. Furthermore, the exact error expressions …

Automatic Objects Removal For Scene Completion, Jianjun Yang, Yin Wang, Honggang Wang, Kun Hua, Wei Wang, Ju Shen

Computer Science Faculty Publications

With the explosive growth of Web-based cameras and mobile devices, billions of photographs are uploaded to the Internet. We can trivially collect a huge number of photo streams for various goals, such as 3D scene reconstruction and other big data applications. However, this is not an easy task due to the fact the retrieved photos are neither aligned nor calibrated. Furthermore, with the occlusion of unexpected foreground objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct realistic scenes. In this paper, we propose a structure-based image completion algorithm for object removal that produces visually …

Seismic Anisotropy And Subduction-Induced Mantle Fabrics Beneath The Arabian And Nubian Plates Adjacent To The Red Sea, Ahmed A. Elsheikh, Stephen S. Gao, Kelly H. Liu, Abdelnasser A. Mohamed, Youqiang Yu, Raafat E. Fat-Helbary

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

For most continental areas, the mechanisms leading to mantle fabrics responsible for the observed anisotropy remain ambiguous, partially due to the lack of sufficient spatial coverage of reliable seismological observations. Here we report the first joint analysis of shear-wave splitting measurements obtained at stations on the Arabian and Nubian Plates adjacent to the Red Sea. More than 1100 pairs of high-quality splitting parameters show dominantly N-S fast orientations at all 47 stations and larger-than-normal splitting times beneath the Afro-Arabian Dome (AAD). The uniformly N-S fast orientations and large splitting times up to 1.5 s are inconsistent with significant contributions from …