Physical Sciences and Mathematics Commons^™

The R Journal (December 2011) 3(2): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Creating and Deploying an Application with (R)Excel and R, Thomas Baier, Erich Neuwirth, and Michele De Meo

glm2: Fitting Generalized Linear Models with Convergence Problems, Ian C. Marschner

Implementing the Compendium Concept with Sweave and DOCSTRIP, Michael Lundholm

Watch Your Spelling! Kurt Hornik and Duncan Murdoch

Ckmeans.1d.dp: Optimal k-means Clustering in One Dimension by Dynamic Programming, Haizhou Wang and Mingzhou Song

Nonparametric Goodness-of-Fit Tests for Discrete Null Distributions, Taylor B. Arnold and John W. Emerson

Using the Google Visualisation API with R, Markus Gesmann and Diego de Castillo

GrapheR: a Multiplatform GUI for Drawing Customizable Graphs in …

Northern Harrier Hatches Mallard Nest, Jeffery W. Stackhouse, Benjamin A. Geaumont

The Prairie Naturalist

The northern harrier (Circus cyaneus) is a widespread raptor commonly found nesting throughout the Northern Great Plains. Northern harriers forage primarily on small mammals and passerines with the males providing the majority of prey to nestlings until 14–28 days of age (Redpath et al. 2006, Vukovich and Ritchison 2006). Although the genus Circus is known to predate eggs from nest of many nesting birds (Hiraldo et al. 1975, Donaszar et al. 1996, Opermanis et al. 2000), few have been recorded commandeering nests of different species (Laine 1928, Fleskes 1992). In June 2010, we observed a northern harrier that …

Synthesis And Characterization Of Acceptor: Donor Block Copolymers For Organic Photovoltaics, Brandon Cory Achord

Dissertations

Mankind needs sources of clean power. Photovoltaic (PV) cells, in use since 1839, have proven reliable and practical for certain applications. PV cell efficiency has changed over the years from 1-2% to ultra-high efficiency cells operating at efficiencies greater than 40%. Organic photovoltaics are a potential transformative technology platform. The potential for cell use, efficiency and cost are all parts of the research and development focus at the time this document was written. This research was initiated with a focus on the synthesis and understanding of the variables effecting acceptor-donor block copolymer. The self-assembled morphology resulting from varying volume ratios …

Personalized Searching For Web Service Using User Interests, Rong Hu, Wanchun Dou, Xiaoqing Frank Liu, Jianxun Liu

Computer Science Faculty Research & Creative Works

Users usually have different prospective even they input a same keyword to search Web services. It is a challenge to personalize web service search engine as more and more keyword-like Web services becoming available on Internet. User interest plays an important role in personalizing search result. Therefore, through interest extraction, Web service search engine is personalized. at last, an experiment is presented to demonstrate the feasibility of the method. © 2011 IEEE.

Book Review Of Encyclopedia Of Biological Invasions, Edited By Daniel Simberloff And Marcel Rejmanek, Qinfeng Guo

The Prairie Naturalist

Book review of Encyclopedia of Biological Invasions, edited by Daniel Simberloff and Marcel Rejmanek.

Species introductions and consequent biotic invasions and homogenization are major components of global change that are drawing increasing concern and various levels of actions and reactions around the world. Invasion ecology has advanced rapidly during the last few decades, and the discipline is now increasingly integrated with the social and economic sciences. A better understanding of the invasion process and its effects is thus clearly needed. For basic research, invasion biology offers fascinating and sometimes unique opportunities for testing certain ecological or evolutionary theories and …

Notes On The Distribution Of Eastern Woodrats And Hispid Cotton Rats In South-Central Nebraska, Heather D. Wills, Keith Geluso, Eric J. Smits, Joseph T. Springer, Wesley E. Newton

The Prairie Naturalist

The eastern woodrat (Neotoma floridana) and hispid cotton rat (Sigmodon hispidus) reach distributional limits in southern Nebraska (Jones 1964, Farney 1975). In the last half-century, both species have expanded their distributional ranges in the region (Kugler and Geluso 2009, Wright et al. 2010). Herein, we report new localities of occurrence for both species that extend known distributional boundaries in south-central Nebraska beyond those reported by Kugler and Geluso (2009) and Wright et al. (2010).

Associated with other studies, we captured small mammals in Sherman live-traps in south-central Nebraska. Voucher specimens were deposited in collections at the …

Three-Dimensionally Preserved Integument Reveals Hydrodynamic Adaptations In The Extinct Marine Lizard Ectenosaurus (Reptilia, Mosasauridae), Johan Lindgren, Michael J. Everhart, Michael W. Caldwell

Sternberg Museum of Natural History Faculty Publications

The physical properties of water and the environment it presents to its inhabitants provide stringent constraints and selection pressures affecting aquatic adaptation and evolution. Mosasaurs (a group of secondarily aquatic reptiles that occupied a broad array of predatory niches in the Cretaceous marine ecosystems about 98-65 million years ago) have traditionally been considered as anguilliform locomotors capable only of generating short bursts of speed during brief ambush pursuits. Here we report on an exceptionally preserved, long-snouted mosasaur (Ectenosaurus clidastoides) from the Santonian (Upper Cretaceous) part of the Smoky Hill Chalk Member of the Niobrara Formation in western Kansas, USA, that …

Perception Of Aquifer Depletion And The Effects Of Land Use Change Across The Madaba Plain, Jordan, Mohammad Salem

Graduate Theses and Dissertations

In Jordan, demand for water for agricultural purposes has put a high strain on aquifer resources. Water mining, erosion, and desertification have all increased as global temperatures rise. This along with fragmentation of the landscape have altered the environment in a profound way. The Madaba Plain was chosen for this study due to the agricultural activities that take place there, as well as the proximity to a number of population centers. The purpose of the study is to examine how fragmentation of irrigated landscape has affected the aquifers underneath, while taking into account perceptions of risk of the local population. …

Removal Of Disinfection By-Product Precursors Using Magnetic Ion Exchange (Miex(R)): The Effects Of Ph And Source Water Variability, Sarah Cousins

Graduate Theses and Dissertations

Disinfection by-products (DBPs) form as an unintended result of drinking water disinfection, from chemical reactions between disinfectants (e.g., free chlorine) and naturally occurring dissolved organic matter (DOM). At present, 11 DBPs are regulated in treated drinking waters due to potential adverse health effects, including four trihalomethanes (THMs). Despite nearly 40 years of DBP research, compliance with DBP regulations remains a challenge for many drinking water treatment plants (DWTPs), including the four DWTPs located on the Beaver Lake Reservoir in Northwest Arkansas. Due to the high net negative surface charge on DOM, anion exchange is one potentially viable method for removing …

Wsrank: A Method For Web Service Ranking In Cloud Environment, Rong Hu, Wanchun Dou, Xiaoqing Frank Liu, Jianxun Liu

Computer Science Faculty Research & Creative Works

For services that have similar functionalities, if they are published by different cloud platforms, it is a challenge to evaluate them, for satisfying different end users' personal preferences. in view of this challenge, a method for web service ranking, named WSRank, is investigated in cloud environment in this paper. It aims at ranking different Web services published by different cloud platforms, taking advantage of Page Rank principle. at last, a case study and experiment are presented to demonstrate the feasibility of the method. © 2011 IEEE.

Middleware For Supporting Content Sharing In Dynamic Networks, Mohan Kumar, Sharma Chakravarthy, Sanjay Kumar Madria, Mark Linderman, Waseem Naqvi

Computer Science Faculty Research & Creative Works

This paper proposes a middleware architecture to enable seamless content sharing in highly dynamic networks, such as those involving a number of aerial unmanned autonomous vehicles (UAVs), which are characterized by constantly changing connectivity and network topology. the proposed middleware maintains up-to-date network status as well as metadata information about data objects in the network nodes, masking the content sharing applications from the network dynamics and faults. Mechanisms for node discovery, message passing, and network management are developed. a strategy is also proposed for efficient replication to ensure availability of data in highly mobile environments. the middleware includes a message …

Develop Energy Dashboard For Real-Time Campus Energy Use Monitoring, Hsui-Lin Winkler, Charlene Hoegler, William Batina

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Lithium In The Upper Centaurus Lupus And Lower Centaurus Crux Subgroups Of Scorpius-Centaurus, Eric J. Bubar, Marc Schaeuble, Jeremy R. King, Eric E. Mamajek, John R. Stauffer

Publications

We utilize spectroscopically derived model atmosphere parameters and the Li i λ6104 subordinate line and the λ6708 doublet to derive lithium abundances for 12 members of the Upper Centaurus Lupus and Lower Centaurus Crux subgroups of the Scorpius–Centaurus OB Association. The results indicate any intrinsic Li scatter in our 0.9–1.4 M stars is limited to ∼0.15 dex, consistent with the lack of dispersion in 1.0 M stars in the 100 Myr Pleiades and 30–50 Myr IC 2391 and 2602 clusters. Both ab initio uncertainty estimates and the derived abundances themselves indicate that the λ6104 line yields abundances with equivalent or …

Ecological Revival And Sustainable Living In The Tropical Dry Evergreen Forest Of Tamil Nadu: A Measurement Of Residential Perception In Sadhana Forest, Elizabeth Collette Mcguire

Department of Environmental Studies: Undergraduate Student Theses

Since 1970, the role and function of the U.S. Environmental Protection Agency (EPA) has been to promote environmental quality and to form strategies for carrying out environmental policy¹. The EPA has committed to sustainability as the next level of environmental protection. The agency states that sustainability calls for policies and strategies that meet society’s present needs without compromising the ability of future generations to meet their own needs². Presently, society’s requirements have resulted in natural resource exploitation and population distention- projected to reach 10 billion people within two human generations³. These paired occurrences are …

Avian Species Abundance In Response To Recreational Trail Use, Carrie A. Wencel

Department of Environmental Studies: Undergraduate Student Theses

Studies have indicated that non-consumptive outdoor recreation may affect wildlife. Thus, as the nation increases interest in outdoor recreation, data suggests the effect on wildlife will also increase. Previous studies indicate that as disturbance to wildlife increases, both avian species richness will decrease. Knowing how to anticipate effects on native species when planning and managing recreational areas is important in order to both provide for human desires and ensure the least impact to local species diversity.

The goal of this project was to observe and compare avian species richness and diversity between selected trail sites within Shevlin Park, Bend, Oregon …

Lake Water Quality, Recreation, & Restoration: The Importance Of Stakeholder Involvement, Biran Gedlinske, Wade Kooiman, Katie Olsen

Other Faculty and Staff Publications

Historically, Iowa’s lakes have been plagued with numerous water quality problems including excessive siltation, nutrients, pesticides, and bacterial contamination. Iowa places a heavy reliance on voluntary efforts to address these problems, largely in the form of best management practices (BMPs). Studies have shown that BMPs can improve lake water quality and, in turn, increase recreational activity and visitor spending. In recognition of the potential economic, recreational, and social benefits of improved lake water quality, the Iowa Department of Natural Resources (IDNR) secured significant legislative funding in 2006 to initiate a state-wide lake restoration program (LRP).

LRP case studies are presented …

Bi-Stability, Hysteresis, And Memory Of Voltage-Gated Lysenin Channels, Daniel Fologea, Eric Krueger, Yuriy I. Mazur, Christine Stith, Yui Okuyama, Ralph Henry, Greg J. Salamo

Physics Faculty Publications and Presentations

Lysenin, a 297 amino acid pore-forming protein extracted from the coelomic fluid of the earthworm E. foetida, inserts constitutively open large conductance channels in natural and artificial lipid membranes containing sphingomyelin. The inserted channels show voltage regulation and slowly close at positive applied voltages. We report on the consequences of slow voltage-induced gating of lysenin channels inserted into a planar Bilayer Lipid Membrane (BLM), and demonstrate that these pore-forming proteins constitute memory elements that manifest gating bi-stability in response to variable external voltages. The hysteresis in macroscopic currents dynamically changes when the time scale of the voltage variation is …

Outlier Detection Using Modified-Ranks And Other Variants, Huaming Huang, Kishan Mehrotra, Chilukuri K. Mohan

Electrical Engineering and Computer Science - Technical Reports

Rank based algorithms provide a promising approach for outlier detection, but currently used rank-based measures of outlier detection suffer from two deficiencies: first they take a large value from an object whose density is high even though the object may not be an outlier and second the distance between the object and its nearest cluster plays a mild role though its rank with respect to its neighbor. To correct for these deficiencies we introduce the concept of modified-rank and propose new algorithms for outlier detection based on this concept.

Characterization Of Enhanced Interferometric Gravitational Wave Detectors And Studies Of Numeric Simulations For Compact-Binary Coalescences, Larne Pekowsky

Physics - Dissertations

Gravitational waves are a consequence of the general theory of relativity. Direct detection of such waves will provide a wealth of information about physics, astronomy, and cosmology. A worldwide effort is currently underway to make the first direct detection of gravitational waves. The global network of detectors includes the Laser Interferometer Gravitational-wave Observatory (LIGO), which recently completed its sixth science run.

A particularly promising source of gravitational waves is a binary system consisting of two neutron stars and/or black holes. As the objects orbit each other they emit gravitational radiation, lose energy, and spiral inwards. This produces a characteristic ``chirp'' …

Controlling Biofouling By Surface Engineering And Molecular Inhibition, Debjyoti Bandyopadhyay

Chemistry - Dissertations

The common theme that binds together all the chapters in this dissertation is anti-biofouling chemistry. By utilizing tools of surface engineering and molecular inhibition, a hypothesis driven, systematic approach of controlling the different forms of biofoulings such as protein adsorption, mammalian cell adhesion and biofilm formation is presented. Chapter 1 provides a brief introduction about topics relevant for understanding the studies presented in subsequent chapters. Chapter 2 reports the synthesis of enantiomerically pure alkanethiols that terminate with different stereoisomer's of sugar alcohols, and the effect of chirality of these polyol-terminated self-assembled monolayers (SAMs) on resisting protein adsorption.

Chapter 3 …

Searching For Gravitational Waves From Compact Binary Coalescence Using Ligo And Virgo Data, Collin Capano

Physics - Dissertations

This thesis describes current efforts to search for gravitational waves from compact binary coalescences (CBCs) by the LIGO Scientific Collaboration (LSC) and the Virgo Collaboration. We briefly review the physics of gravitational-wave emission and detection, describing how gravitational waves are emitted from "inspiraling" compact stellar mass objects and how the LSC and Virgo try to detect them using interferometers. Next we review the data-analysis principles used to search for potential signals in the detectors' noise. These principles are employed by ``ihope," which is the data-analysis pipeline used to search for CBCs. We describe each step in this pipeline and discuss …

Data-Intensive Computing For Bioinformatics Using Virtualization Technologies And Hpc Infrastructures, Pengfei Xuan

All Theses

The bioinformatics applications often involve many computational components and massive data sets, which are very difficult to be deployed on a single computing machine. In this thesis, we designed a data-intensive computing platform for bioinformatics applications using virtualization technologies and high performance computing (HPC) infrastructures with the concept of multi-tier architecture, which can seamlessly integrate the web user interface (presentation tier), scientific workflow (logic tier) and computing infrastructure (data/computing tier). We demonstrated our platform on two bioinformatics projects. First, we redesigned and deployed the cotton marker database (CMD) (http://www.cottonmarker.org), a centralized web portal in the cotton research community, using the …

Enhancing Inettest By Improving The Programming Question And Group Grading, Sushil Dosi

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

This report describes an improvement to the Utah State University iNetTest testing system. The iNetTest system allows instructors and/or students to: • Create/take tests with rich sets of question types (multiple choice, essay, true/false, computational programming question, etc.); • Monitor the test takers for cheating; • Auto-grade for many types of questions, as well as group grade for all question types; and • Send scores to students via either email or SMS. Specifically, this report discusses the design and development of an improved computational programming question for the iNetTest system. For programming questions, iNetTest allows for the use of various …

Foreign Private Investment And Economic Growth In Nigeria: A Cointegrated Var And Granger Causality Analysis, F. Z. Abdullahi, S. Ladan, Haruna R. Bakari

CBN Journal of Applied Statistics (JAS)

This research uses a cointegration VAR model to study the contemporaneous long-run dynamics of the impact of Foreign Private Investment (FPI), Interest Rate (INR) and Inflation rate (IFR) on Growth Domestic Products (GDP) in Nigeria for the period January 1970 to December 2009. The Unit Root Test suggests that all the variables are integrated of order 1. The VAR model was appropriately identified using AIC information criteria and the VECM model has exactly one cointegration relation. The study further investigates the causal relationship using the Granger causality analysis of VECM which indicates a uni-directional causality relationship between GDP and FDI …

Benthic Habitat Characterization For The South Florida Ocean Measurement Facility (Sfomf), David S. Gilliam, Brian K. Walker

Marine & Environmental Sciences Faculty Reports

This report summarizes the distribution and relative abundance of two stony coral species (Acropora cervicornis and Acropora palmata) currently listed as threatened under the US Endangered Species Act (ESA) (Federal Register/Vol. 71, No. 129/Thursday, July 6, 2006 / Rules and Regulations, http://www.gpo.gov/fdsys/pkg/FR-2006-07-06/pdf/06-6017.pdf) and seven additional stony coral species which have been petitioned for listing as endangered or threatened under the ESA (Agaricia lamarcki, Dendrogyra cylindrus, Dichocoenia stokesii, Montastraea annularis, Montastraea faveolata, Montastraea franksi, and Mycetophyllia ferox) (Federal Register/Vol. 75, No. 27/Wednesday, February 10, 2010/Proposed Rules, http://www.nmfs.noaa.gov/pr/pdfs/fr/fr75-6616.pdf). This report also summarizes the abundance and distribution …

Estimating Oil Concentration And Flow Rate With Calibrated Vessel-Mounted Acoustic Echo Sounders, Thomas C. Weber, Alex De Robertis, Shep Smith, Samuel F. Greenaway, Larry A. Mayer, Glen Rice

Center for Coastal and Ocean Mapping

As part of a larger program aimed at evaluating acoustic techniques for mapping the distribution of subsurface oil and gas associated with the Deepwater Horizon-Macondo oil spill, observations were made on June 24 and 25, 2010 using vessel-mounted calibrated single-beam echo sounders on the National Oceanic and Atmospheric Administration ship Thomas Jefferson. Coincident with visual observations of oil at the sea surface, the 200-kHz echo sounder showed anomalously high-volume scattering strength in the upper 200 m on the western side of the wellhead, more than 100 times higher than the surrounding waters at 1,800-m distance from the wellhead, …

A General Family Of Dual To Ratio-Cum-Product Estimator In Sample Surveys, Florentin Smarandache, Rajesh Singh, Mukesh Kumar, Pankaj Chauhan, Nirmala Sawan

Branch Mathematics and Statistics Faculty and Staff Publications

This paper presents a family of dual to ratio-cum-product estimators for the finite population mean. Under simple random sampling without replacement (SRSWOR) scheme, expressions of the bias and mean-squared error (MSE) up to the first order of approximation are derived. We show that the proposed family is more efficient than usual unbiased estimator, ratio estimator, product estimator, Singh estimator (1967), Srivenkataramana (1980) and Bandyopadhyaya estimator (1980) and Singh et al. (2005) estimator. An empirical study is carried out to illustrate the performance of the constructed estimator over others.

Patterns Of Age-0 Gizzard Shad Abundance And Food Habits In A Nebraska Irrigation Reservoir, Christopher L. Sullivan, Casey W. Schoenebeck, Keith D. Koupal, W. Wyatt Hoback, Brian C. Peterson

The Prairie Naturalist

Gizzard shad (Dorosoma cepedianum) are prolific spawners that can influence reservoir communities. Larval gizzard shad may compete with larval recreational fish for zooplankton resources. Therefore, it is necessary to determine larval gizzard shad dynamics and food habits to better understand their potential for competition with larval recreational fish. Our study examined age-0 gizzard shad abundance in Harlan County Reservoir during late spring/summer from 2002–2010 and food habits and prey electivity of age-0 gizzard shad during late spring/summer 2008 and 2009. The annual peak age-0 gizzard shad density 3 from 2002–2010 ranged from 50 to 380/100 m , which …

Late Seasonal Captures Of The Plains Pocket Mouse (Perognathus Flavescens) In Iowa, Hans W. Otto, Jeremy A. White

The Prairie Naturalist

The plains pocket mouse, Perognathus flavescens, is a nocturnal granivore that inhabits friable soils in sparsely vegetated areas (Monk and Jones 1996). In the United States, the distribution of the plains pocket mouse extends from Arizona, New Mexico, and Texas through the Great Plains to North Dakota and Minnesota (Hall 1981). This species reaches its easternmost limits in Iowa, where it has been documented from a limited number of grassland sites in eastern, central, and western parts of the state (Bowles 1975, Wilson et al. 1996). Due to loss of grassland habitat, the plains pocket mouse is currently listed …

Book Review: Effects Of Climate Change On Birds, Edited By Anders Pape Meller, Wolfgang Fiedler, And Peter Berthold, Brian J. Olsen

The Prairie Naturalist

Book review of Effects of Climate Change on Birds, edited by Anders Pape Meller, Wolfgang Fiedler, and Peter Berthold.

Climate scientists from across the globe predict vast changes during the next century in the planet's temperatures, precipitation, storm intensities, fire regimes, hydrologic cycles, and atmospheric, water, and soil chemistries. The changes will be global, but their effects will be felt locally everywhere. To find a scientifically and socially engaging bellwether of these events, we need to look only through the lens of avian biology. Birds are found from pole to pole; their movements connect continents. They are loud, colorful …