Computer Sciences Commons^™

Brainr: Interactive 3 And 4d Images Of High Resolution Neuroimage Data, John Muscelli, Elizabeth Sweeney, Ciprian Crainiceanu

The R Journal

We provide software tools for displaying and publishing interactive 3-dimensional (3D) and 4-dimensional (4D) figures to html webpages, with examples of high-resolution brain imaging. Our framework is based in the R statistical software using the rgl package, a 3D graphics library. We build on this package to allow manipulation of figures including rotation and translation, zooming, coloring of brain substructures, adjusting transparency levels, and addition/or removal of brain structures. The need for better visualization tools of ultra high dimensional data is ever present; we are providing a clean, simple, web-based option. We also provide a package (brainR) for …

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 …

Decaf: A New Event Detection Logic For The Purpose Of Fusing Delineated-Continuous Spatial Information, Kerry Q. Hart

School of Computing: Dissertations, Theses, and Student Research

Geospatial information fusion is the process of synthesizing information from complementary data sources located at different points in space and time. Spatial phenomena are often measured at discrete locations by sensor networks, technicians, and volunteers; yet decisions often require information about locations where direct measurements do not exist. Traditional methods assume the spatial phenomena to be either discrete or continuous, an assumption that underlies and informs all subsequent analysis. Yet certain phenomena defy this dichotomy, alternating as they move across spatial and temporal scales. Precipitation, for example, appears continuous at large scales, but it can be temporally decomposed into discrete …

Variable Bounds Analysis Of A Climate Model Using Software Verification Techniques, Peter Revesz, Robert Woodward

School of Computing: Conference and Workshop Papers

Software verification techniques often use some approximation method that identifies the limits of the possible range of values that variables in a computer program can take during execution. Current climate models are complex computer programs that are typically iterated time-step by time-step to predict the next value of the climate-related variables. Because these iterative methods are necessarily computed only for a fixed number of iterations, they are unable to answer many long-range questions that may be posed regarding climate change, for example, whether there are natural fluctuations or whether a tipping point is reached after which there is no return …

A Self-Adaptive Framework For Failure Avoidance In Configurable Software, Jacob Swanson

School of Computing: Dissertations, Theses, and Student Research

Many software systems today are highly-configurable, meaning the user can customize their instance of the application, adding and removing features as needed. However, this configurability makes it harder to ensure that faults will not escape testing and manifest as failures in the field. This is because many failures are configuration-dependent; they will appear under certain combinations of features configurations, but not others. Once faults are found and reported in the field, there can be a long lag time (days, weeks or even months) until patches are created and released to fix them. In the meantime, users will continue to use …

Providing Flexible File-Level Data Filtering For Big Data Analytics, Lei Xu, Ziling Huang, Hong Jiang, Lei Tian, David Swanson

School of Computing: Technical Reports

The enormous amount of big data datasets impose the needs for effective data filtering technique to accelerate the analytics process. We propose a Versatile Searchable File System, VSFS, which provides a transparent, flexible and near real-time file-level data filtering service by searching files directly through the file system. Therefore, big data analytics applications can transparently utilize this filtering service without application modifications. A versatile index scheme is designed to adapt to the exploratory and ad-hoc nature of the big data analytics activities. Moreover, VSFS uses a RAM-based distributed architecture to perform file indexing. The evaluations driven by three real-world analytics …

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Functional Evolution Of Plp-Dependent Enzymes Based On Active-Site Structural Similarities, Jonathan Catazaro, Adam Caprez, Ashu Guru, David Swanson, Robert Powers

Holland Computing Center: Faculty Publications

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can …

Cms Use Of A Data Federation, Kenneth A. Bloom, C.

Kenneth Bloom Publications

CMS is in the process of deploying an Xrootd based infrastructure to facilitate a global data federation. The services of the federation are available to export data from half the physical capacity and the majority of sites are configured to read data over the federation as a back-up. CMS began with a relatively modest set of use-cases for recovery of failed local file opens, debugging and visualization. CMS is finding that the data federation can be used to support small scale analysis and load balancing. Looking forward we see potential in using the federation to provide more flexibility in the …

Yeast Pheromone Pathway Modeling Using Petri Nets, Stephen D. Scott, Abhishek Majumdar, Jitender S. Deogun, Steven D. Harris

School of Computing: Conference and Workshop Papers

Background: Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a …

A Comparison Of A Campus Cluster And Open Science Grid Platforms For Protein- Guided Assembly Using Pegasus Workflow Management System, Natasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Campbell, Harkamal Walia, Jitender S. Deogun

School of Computing: Conference and Workshop Papers

Scientific workflows are a useful tool for managing large and complex computational tasks. Due to its intensive resource requirements, the scientific workflows are often executed on distributed platforms, including campus clusters, grids and clouds. In this paper we build a scientific workflow for blast2cap3, the protein-guided assembly, using the Pegasus Workflow Management System (Pegasus WMS). The modularity of blast2cap3 allows us to decompose the existing serial approach on multiple tasks, some of which can be run in parallel. Afterwards, this workflow is deployed on two distributed execution platforms: Sandhills, the University of Nebraska Campus Cluster, and the Open Science …

Transforming Web Tables To A Relational Database, David W. Embley, George Nagy, Sharad C. Seth

School of Computing: Conference and Workshop Papers

HTML tables represent a significant fraction of web data. The often complex headers of such tables are determined accurately using their indexing property. Isolated headers are factored to extract category hierarchies. Web tables are then transformed into a canonical form and imported into a relational database. The proposed processing allows for the formulation of arbitrary SQL queries over the collection of induced relational tables.

Information In Biological Systems And The Fluctuation Theorem, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.

Understanding Human Learning Using A Multiagent Based Unified Learning Model Simulation, Vlad T. Chiriacescu

School of Computing: Dissertations, Theses, and Student Research

Within cognitive science, computational modeling based on cognitive architectures has been an important approach to addressing questions of human cognition and learning. Modeling issues such as limited expressivity in representing knowledge and lack of appropriate selection of model structure represent a challenge for existing architectures. Furthermore, latest research shows that the concepts of long-term memory, motivation and working memory are critical cognitive aspects but a unifying cognitive paradigm integrating those concepts hasn’t been previously achieved.

Derived from a synthesis of neuroscience, cognitive science, psychology, and education, the Unified Learning Model (ULM) provides this integration by merging a statistical learning mechanism …

The R Journal (December 2013) 5(2): Complete Issue, The R Foundation

The R Journal

Editorial, Hadley Wickham

Contributed Research Articles

factorplot: Improving Presentation of Simple Contrasts in Generalized Linear Models, David A. Armstrong II

spMC: Modelling Spatial Random Fields with Continuous Lag Markov Chains, Luca Sartore

RNetCDF: A Package for Reading and Writing NetCDF Datasets, Pavel Michna and Milton Woods

Surface Melting Curve Analysis with R, Stefan Rödiger, Alexander Böhm and Ingolf Schimke

Performance Attribution for Equity Portfolios, Yang Lu and David Kane

ExactCIdiff: An R Package for Computing Exact Confidence Intervals for the Difference of Two Proportions, Guogen Shan and Weizhen Wang

rlme: An R Package for Rank-Based Estimation and Prediction in Random …