Computer Sciences Commons^™

R Packages To Aid In Handling Web Access Logs, Oliver Keyes, Bob Rudis, Jay Jacobs

The R Journal

Web access logs contain information on HTTP(S) requests and form a key part of both industry and academic explorations of human behaviour on the internet. But the preparation (reading, parsing and manipulation) of that data is just unique enough to make generalized tools unfit for the task, both in programming time and processing time which are compounded when dealing with large data sets common with web access logs. In this paper we explain and demonstrate a series of packages designed to efficiently read in, parse and munge access log data, allowing researchers to handle URLs and IP addresses easily. These …

An Interactive Survey Application For Validating Social Network Analysis Techniques, Mitchell Joblin, Wolfgang Mauerer

The R Journal

Social network analysis is extremely well supported by the R community and is routinely used for studying the relationships between people engaged in collaborative activities. While there has been rapid development of new approaches and metrics in this field, the challenging question of validity (how well insights derived from social networks agree with reality) is often difficult to address. We propose the use of several R packages to generate interactive surveys that are specifically well suited for validating social network analyses. Using our web-based survey application, we were able to validate the results of applying community-detection algorithms to infer the …

Conference Report: User! 2016, Joe Rickert

The R Journal

The 12th international R user conference, useR! 2016, took place at Stanford University, Stanford CA fromJune27throughJune30th. Hosted by the Stanford University Department of Statistics and the Stanford Libraries, the conference took place at the Frances Arrillaga Alumni Center, on the surrounding lawns and in several adjacent buildings. The floor to ceiling windows of the larger conference rooms, the garden locations for coffee and meals and the beautiful weather contributed to making the event a classic California experience.

Schemaonread: A Package For Schema-On-Read In R, Michael J. North

The R Journal

SchemaOnRead is a CRAN package that provides an extensible mechanism for importing a wide range of file types into R as well as support for the emerging schema-on-read paradigm in R. The schema-on-read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements. The provided tools can be used as-is or easily customized to implement tool chains …

Keyplayer: An R Package For Locating Key Players In Social Networks, Weihua An, Yu-Hsin Liu

The R Journal

Interest in social network analysis has exploded in the past few years, partly thanks to the advancements in statistical methods and computing for network analysis. A wide range of the methods for network analysis is already covered by existent R packages. However, no comprehensive packages are available to calculate group centrality scores and to identify key players (i.e., those players who constitute the most central group) in a network. These functionalities are important because, for example, many social and health interventions rely on key players to facilitate the intervention. Identifying key players is challenging because players who are individually the …

Rtableicc: An R Package For Random Generation Of 22k And Rc Contingency Tables, Haydar Demirhan

The R Journal

In this paper, we describe the R package rTableICC that provides an interface for random generation of 2 2 K and R Ccontingency tables constructed over either intraclass-correlated or uncorrelated individuals. Intraclass correlations arise in studies where sampling units include more than one individual and these individuals are correlated. The package implements random generation of contingency tables over individuals with or without intraclass correlations under various sampling plans. The package include two functions for the generation of K 2 2 tables over product-multinomial sampling schemes and that of 2 2 K tables under Poisson or multinomial sampling plans. It also …

Crowdsourced Data Preprocessing With R And Amazon Mechanical Turk, Thomas J. Leeper

The R Journal

This article introduces the use of the Amazon Mechanical Turk (MTurk) crowdsourcing platform as a resource for R users to leverage crowdsourced human intelligence for preprocessing “messy” data into a form easily analyzed within R. The article first describes MTurk and the MTurkR package, then outlines how to use MTurkR to gather and manage crowdsourced data with MTurk using some of the package’s core functionality. Potential applications of MTurkR include construction of manually coded training sets, human transcription and translation, manual data scraping from scanned documents, content analysis, image classification, and the completion of online survey questionnaires, among others. As …

Exploring Interaction Effects In Two-Factor Studies Using The Hiddenf Package In R., Christopher Franck, Jason A. Osborne

The R Journal

In crossed, two-factor studies with one observation per factor-level combination, interaction effects between factors can be hard to detect and can make the choice of a suitable statistical model difficult. This article describes hiddenf, an R package that enables users to quantify and characterize a certain form of interaction in two-factor layouts. When effects of one factor (a) fall into two groups depending on the level of another factor, and (b) are constant within these groups, the interaction pattern is deemed "hidden additivity" because within groups, the effects of the two factors are additive, while between groups the factors …

Gmdh: An R Package For Short Term Forecasting Via Gmdh-Type Neural Network Algorithms, Osman Dag, Ceylan Yozgatligil

The R Journal

Group Method of Data Handling (GMDH)-type neural network algorithms are the heuristic self organization method for the modelling of complex systems. GMDH algorithms are utilized for a variety of purposes, examples include identification of physical laws, the extrapolation of physical fields, pattern recognition, clustering, the approximation of multidimensional processes, forecasting without models, etc. In this study, the R package GMDH is presented to make short term forecasting through GMDH-type neural network algorithms. The GMDH package has options to use different transfer functions (sigmoid, radial basis, polynomial, and tangent functions) simultaneously or separately. Data on cancer death rate of Pennsylvania from …

The R Journal (August 2016) 8(1): Complete Issue, The R Foundation

The R Journal

Editorial, Michael Lawrence

Contributed Research Articles

metaplus: An R Package for the Analysis of Robust Meta-Analysis and Meta-Regression, Ken J. Beath

Gender Prediction Methods Based on First Names with genderizeR, Kamil Wais

Conditional Fractional Gaussian Fields with the Package FieldSim, Alexandre Brouste, Jacques Istas, and Sophie Lambert-Lacroix

rTableICC: An R Package for Random Generation of 22K and RC Contingency Tables, Haydar Demirhan

Maps, Coordinate Reference Systems and Visualising Geographic Data with mapmisc, Patrick E. Brown

Variable Clustering in High-Dimensional Linear Regression: The R Package clere, Loïc Yengo, Julien Jacques, Christophe Biernacki, and Mickael Canouil

Stylometry with R: A Package for …

Improving The Efficiency Of Ci With Uber-Commits, Matias Waterloo

School of Computing: Dissertations, Theses, and Student Research

Continuous Integration (CI) is a software engineering practice where developers break their coding tasks into small changes that can be integrated with the shared code repository on a frequent basis. The primary objectives of CI are to avoid integration problems caused by large change sets and to provide prompt developer feedback so that if a problem is detected, it can be easily and quickly resolved. In this thesis, we argue that while keeping changes small and integrating often is a wise approach for developers, the CI server may be more efficient operating on a different scale. In our approach, the …

An Extendable Visualization And User Interface Design For Time-Varying Multivariate Geoscience Data, Yanfu Zhou

School of Computing: Dissertations, Theses, and Student Research

Geoscience data has unique and complex data structures, and its visualization has been challenging due to a lack of effective data models and visual representations to tackle the heterogeneity of geoscience data. In today’s big data era, the needs of visualizing geoscience data become urgent, especially driven by its potential value to human societies, such as environmental disaster prediction, urban growth simulation, and so on. In this thesis, I created a novel geoscience data visualization framework and applied interface automata theory to geoscience data visualization tasks. The framework can support heterogeneous geoscience data and facilitate data operations. The interface automata …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene

School of Computing: Dissertations, Theses, and Student Research

Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins …

Significant Permission Identification For Android Malware Detection, Lichao Sun

School of Computing: Dissertations, Theses, and Student Research

A recent report indicates that a newly developed malicious app for Android is introduced every 11 seconds. To combat this alarming rate of malware creation, we need a scalable malware detection approach that is effective and efficient. In this thesis, we introduce SigPID, a malware detection system based on permission analysis to cope with the rapid increase in the number of Android malware. Instead of analyzing all 135 Android permissions, our approach applies 3-level pruning by mining the permission data to identify only significant permissions that can be effective in distinguishing benign and malicious apps. Based on the identified significant …

Examining Bridges Between Informal And Formal Learning Environments: A Sequential Mixed Method Design, Dagen L. Valentine

Department of Agricultural Leadership, Education, and Communication: Dissertations, Theses, and Student Research

The purpose of this sequential mixed method study was to identify schools implementing a technology-based engineering design intervention in a way that connects or bridges formal learning environments of the school-day to informal learning environments such as afterschool programs. Further, this study investigated educators’ decisions that enabled or facilitated bridging between formal and informal learning environments. This cooperation and/or linking between informal and formal learning time is bridging. Participants included public schools (n=16) in Eastern Nebraska that incorporated the Nebraska Wearables Technology (WearTec) program at their school, club or Out-of-School-Time program during the 2015-2016 school year. Three of the schools …

Spica: Stereographic Projection For Interactive Crystallographic Analysis, Xingzhong Li

Nebraska Center for Materials and Nanoscience: Faculty Publications

In numerous research fields, especially the applications of electron and X-ray diffraction, stereographic projection represents a powerful tool for researchers. SPICA is a new computer program for stereographic projection in interactive crystallographic analysis, which inherits features from the previous JECP/SP and includes more functions for extensive crystallographic analysis. SPICA provides fully interactive options for users to plot stereograms of crystal directions and crystal planes, traces, and Kikuchi maps for an arbitrary crystal structure; it can be used to explore the orientation relationships between two crystalline phases with a composite stereogram; it is also used to predict the tilt angles of …

Estimability Tools For Package Developers, Russell V. Lenth

The R Journal

When a linear model is rank-deficient, then predictions based on that model become questionable because not all predictions are uniquely estimable. However, some of them are, and the estimability package provides tools that package developers can use to tell which is which. With the use of these tools, a model object’s predict method could return estimable predictions as-is while f lagging non-estimable ones in some way, so that the user can know which predictions to believe. The estimability package also provides, as a demonstration, an estimability-enhanced epredict method to use in place of predict for models fitted using the stats …

Why Do Record/Replay Tests Of Web Applications Break?, Mouna Hammoudi

School of Computing: Dissertations, Theses, and Student Research

Software engineers often use record/replay tools to enable the automated testing of web applications. Tests created in this manner can then be used to regression test new versions of the web applications as they evolve. Web application tests recorded by record/replay tools, however, can be quite brittle; they can easily break as applications change. For this reason, researchers have begun to seek approaches for automatically repairing record/replay tests. To date, however, there have been no comprehensive attempts to characterize the causes of breakages in record/replay tests for web applications. In this work, we present a taxonomy classifying the ways in …

Sonifying Git History, Kevin J. North

School of Computing: Dissertations, Theses, and Student Research

Version control is a technique that software developers use in industry to manage their source code artifacts. One benefit of using version control is that it produces a history of every change made to a codebase, which developers frequently analyze in order to aid the software development process. However, version control history contains highly multidimensional and temporal data. State of the art techniques can show several of these dimensions, but they cannot show a large number of dimensions simultaneously without becoming difficult to understand. An alternative technique to understand temporal data with high dimensionality is sonification. Sonification maps information to …

A Roadmap To Safe And Reliable Engineered Biological Nano-Communication Networks, Justin W. Firestone

School of Computing: Dissertations, Theses, and Student Research

Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell's core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened …

Chipathlon: A Competitive Assessment For Gene Regulation Tools, Avi Knecht, Adam Caprez, Istvan Ladunga

UCARE: Research Products

When gene regulation of the cell cycle malfunctions, it frequently causes cancer.

Adult, differentiated cells can be reprogrammed to induced pluripotent stem cell; which can then be reprogrammed to heart muscle, skin, etc, to repair damaged tissue (to limited extent in clinical practice).

ChIPathlon: Evaluate the performance of all transcription factor mapping (peak calling) methods. To this end, we will develop a scalable and easy to use super computing pipeline to stage data, compare many different peak calling and differential binding site tools, and store all results into a single database.

Flying By Fire: Making Controlled Burns Safer For Humans And Uavs, Rebecca Horzewski, Carrick Detweiler

UCARE: Research Products

A temperature sensing circuit board was developed that will allow Nimbus Lab's controlled burn starting UAV to react to the temperatures around it.

Alignment For Comprehensive Two-Dimensional Gas Chromatography (Gcxgc) With Global, Low-Order Polynomial Transformations, Davis Rempe, Stephen Reichenbach, Stephen Scott

UCARE: Research Products

As columns age and differ between systems, retention times for GC x GC may vary between runs. In order to properly analyze chromatograms, it is often desirable to align chromatographic features between chromatograms. This alignment can be characterized by a mapping of retention times from one chromatogram to the retention times of another chromatogram. Alignment methods can be classified as global or local, i.e., whether the geometric differences between chromatograms are characterized by a single function for the entire chromatogram or by a combination of many functions for different regions of the chromatogram. Previous work has shown that global, low-degree …

Past Meets Future: Combining Gis, 3d Technologies, And Legacy Data To Reanalyze Ceramics At Copan, Honduras, Stephanie Sterling, Heather Richards-Rissetto, René Viel

UCARE: Research Products

The archaeological site of Copán—a UNESCO World Heritage Site in Honduras—was a primary center for cultural and economic exchange in the Maya world from the fifth to ninth centuries. Our research investigates the sociopolitical climate of the city immediately preceding this collapse. This poster presents the results of a pilot study intended to evaluate the potential of using a combination of digital technologies and legacy data to reanalyze a subset of diagnostic ceramics from select sites outside of Copan’s urban core. Our methods involved:

(1) Applying photogrammetry to generate 3D models for approximately 30 potentially temporally-diagnostic ceramic types

(2) Digitizing, …

A Mitochondrial Dna-Based Computational Model Of The Spread Of Human Populations, Peter Revesz

School of Computing: Faculty Publications

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in …

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

Image Harvest: An Open-Source Platform For High-Throughput Plant Image Processing And Analysis, Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David R. Swanson, Harkamal Walia

Holland Computing Center: Faculty Publications

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources …

The Unforeseen Evolution Of Technology, Dylan White

Nebraska College Preparatory Academy: Senior Capstone Projects

Technology has evolved in the past two decades to alter how countries and their people live in the present day. Said technology has also both solved and created new problems for world powers (i.e. the U.S. and China) to face. Issues of cyber security and cyber surveillance are already potential problems that need to be addressed, where topics like cyber warfare need to be closely monitored with time. All of these are potentially underestimated threats to civil liberties, and to countries in their entirety.

I agree with the findings in my project… • The United States is a model to …

Interim Report, Hd-51897-14, Image Analysis For Archival Discovery (Aida), January 2016, Elizabeth M. Lorang, Leen-Kiat Soh

CDRH Grant Reports

In the third six months of work on "Image Analysis for Archival Discovery," the project team has made progress toward the goals outlined in our report from June 2015. As we reported in June 2015, we realized that our original plan to analyze 7 million pages from Chronicling America was overly ambitious for the grant period, and we revised our goal to complete a thorough case study of our methodology and code for all newspaper images in Chronicling America from the period 1836-1840. Activities undertaken, toward this and other grant goals, from June 2015–December 2015:

• Publication of the article, "Developing …

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