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A Simulation-Based Approach For Evaluating Gene Expression Analyses, Carly Ruth Pendleton Mar 2007

A Simulation-Based Approach For Evaluating Gene Expression Analyses, Carly Ruth Pendleton

Theses and Dissertations

Microarrays enable biologists to measure differences in gene expression in thousands of genes simultaneously. The data produced by microarrays present a statistical challenge, one which has been met both by new modifications of existing methods and by completely new approaches. One of the difficulties with a new approach to microarray analysis is validating the method's power and sensitivity. A simulation study could provide such validation by simulating gene expression data and investigating the method's response to changes in the data; however, due to the complex dependencies and interactions found in gene expression data, such a simulation would be complicated and …

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Solute Chemistry And Isotopic Investigation Of The Groundwater Flow Paths In Honey Lake Basin, Lassen County, California And Washoe County, Nevada, Rachel M. Henderson Mar 2007

Solute Chemistry And Isotopic Investigation Of The Groundwater Flow Paths In Honey Lake Basin, Lassen County, California And Washoe County, Nevada, Rachel M. Henderson

Theses and Dissertations

Honey Lake Basin is a large, hydrologically closed valley with two playa lakes that are separated by a low elevation sill. The Basin has a complex hydrogeologic setting, with numerous groundwater flow paths that interact with surface waters and three basic aquifers; shallow, deep, and geothermal. Thirteen flow paths; eleven cold and two thermal, are identified and the geochemical evolution of those paths are characterized by integrating solute chemistry and isotopic data. The chemical flow paths include recharge in either granitoid or volcanic terrains in the Sierra Nevada Range and the Modoc Plateau, respectively. The groundwater then flows through alluvial …

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Calibration Procedure For A Microscopic Traffic Simulation Model, Carole Turley Mar 2007

Calibration Procedure For A Microscopic Traffic Simulation Model, Carole Turley

Theses and Dissertations

The inputs to a microscopic traffic simulation model generally include quantitative, but immeasurable data describing driver behavior and vehicle performance characteristics. Engineers often use default values for parameters such as car-following sensitivity and gap acceptance because it can be difficult to obtain accurate estimates for these parameters. While recent research has indicated that the accuracy of a simulation model can significantly improve if driver behavior parameters are calibrated to local data, this is not a typical practice. Manual calibration of these parameters is often too time-consuming to be cost-effective. Researchers have applied automated calibration procedures using genetic algorithms to these …

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Semi Autonomous Vehicle Intelligence: Real Time Target Tracking For Vision Guided Autonomous Vehicles, Jonathan D. Anderson Mar 2007

Semi Autonomous Vehicle Intelligence: Real Time Target Tracking For Vision Guided Autonomous Vehicles, Jonathan D. Anderson

Theses and Dissertations

Unmanned vehicles (UVs) are seeing more widespread use in military, scientific, and civil sectors in recent years. These UVs range from unmanned air and ground vehicles to surface and underwater vehicles. Each of these different UVs has its own inherent strengths and weaknesses, from payload to freedom of movement. Research in this field is growing primarily because of the National Defense Act of 2001 mandating that one-third of all military vehicles be unmanned by 2015. Research using small UVs, in particular, is a growing because small UVs can go places that may be too dangerous for humans. Because of the …

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Pre-Historic Landslides On The Southeast Flank Of The Uinta Mountains, Utah: Character And Causes Of Slope Failure, Todd D. Bradfield Mar 2007

Pre-Historic Landslides On The Southeast Flank Of The Uinta Mountains, Utah: Character And Causes Of Slope Failure, Todd D. Bradfield

Theses and Dissertations

More than 100 landslides have been mapped along the southeast flank of the Uinta Mountains. Large landslide deposits are up to 4.6 kilometers long and have an area of approximately 5-9 km². Landslide types include multiple and successive rock slumps, debris slumps and debris flows. Most landslides have a main head scarp in the Bishop Conglomerate and the large landslides have many minor scarps. Multiple slump blocks are manifest by repeated transverse ridges and trenches in the head area of some landslides. Most body and toe areas are deeply incised by gully erosion (up to 91 meters deep) and drainages …

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Structure And Nitrogen Chemistry In Coal, Biomass, And Cofiring Low-Nox Flames, Bradley David Damstedt Mar 2007

Structure And Nitrogen Chemistry In Coal, Biomass, And Cofiring Low-Nox Flames, Bradley David Damstedt

Theses and Dissertations

Addressing global climate change will require increasing sustainable energy usage. Cofiring biomass fuels with coal for electrical power generation is an efficient, cost effective method of CO2 mitigation. This work is an experimental investigation of the flame structure and nitrogen chemistry differences occurring between coal, biomass and cofiring flames. A pilot-scale facility was fired with a dual-feed low-NOx burner capable of independently conveying 2 separate fuels unblended to the burner. Spatially detailed gas species measurements were made for 8 flames, including a coal, straw, finely ground straw, wood, and 4 straw/coal cofiring flames. Particle samples were also obtained from 5 …

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Structural Analysis Of Rock Canyon Near Provo, Utah, Laura Cardon Wald Mar 2007

Structural Analysis Of Rock Canyon Near Provo, Utah, Laura Cardon Wald

Theses and Dissertations

A detailed structural study of Rock Canyon (near Provo, Utah) provides insight into Wasatch Range tectonics and fold-thrust belt kinematics. Excellent exposures along the E-W trending canyon allow the use of digital photography in conjunction with traditional field methods for a thorough analysis of Rock Canyon's structural features. Detailed photomontages and geometric and kinematic analyses of some structural features help to pinpoint deformation mechanisms active during the canyon's tectonic history. Large-scale images and these structural data are synthesized in a balanced cross section, which is used to reconstruct the structural evolution of this portion of the range. Projection of surficial …

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Parameter Importance Of An Analytical Model For Transport In The Vadose Zone, Tanner Hans Bushnell Mar 2007

Parameter Importance Of An Analytical Model For Transport In The Vadose Zone, Tanner Hans Bushnell

Theses and Dissertations

The American Society of Testing and Materials (ASTM) has established a three tier risk-based corrective action (RBCA) program for cleaning up petroleum release sites, which is supported by the Environmental Protection Agency. RBCA programs make the cleanup of spill sites more efficient by requiring additional site information only when a more accurate risk assessment is needed. For spill sites that do not pass the first tier general assessment, a Tier 2 evaluation involving site specific information and screening level models to assess the potential risk must be conducted. Screening level models generally require site specific input parameters. To increase efficiency …

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A High-Resolution Microscopic Electrical Impedance Imaging Modality: Scanning Impedance Imaging, Hongze Liu Mar 2007

A High-Resolution Microscopic Electrical Impedance Imaging Modality: Scanning Impedance Imaging, Hongze Liu

Theses and Dissertations

Electrical impedance imaging is an imaging technique which has the capability of revealing the spatial distribution of the electrical impedance inside biological tissues. Classical electrical impedance imaging including Electrical Impedance Tomography (EIT) typically has low resolution. Advances in electrical impedance imaging typically involve methods that either increase image resolution or image contrast. This study investigates the possibility of the resolution improvement for electrical impedance imaging using motion, and presents a novel high-resolution and calibrated impedance imaging method called Scanning electrical Impedance Imaging (SII). SII uses an electrical probe held at a known voltage and scanned over a thin sample immersed …

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The Origins Of Four Paterae Of Malea Planum, Mars, Susan K. Larson Mar 2007

The Origins Of Four Paterae Of Malea Planum, Mars, Susan K. Larson

Theses and Dissertations

Malea Planum is a volcanic plain on the southern rim of Hellas Planitia, the largest impact basin on Mars. Four large circular structures on Malea Planum have traditionally been identified as paterae, or low relief, central vent volcanoes (Plescia and Saunders, 1979). A geologic map was constructed and new crater counts made to explore the ages and origins of the paterae. Amphitrites and Peneus Paterae have radial patterns of wrinkle ridges on their flanks and distinct summit calderas (95 km and 130 km across) with arcuate bounding scarps. In contrast, Malea and Pityusa Paterae are broad depressions with diameters greater …

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Spot Friction Welding Of Ultra High-Strength Automotive Sheet Steel, Jack H. Sederstrom Mar 2007

Spot Friction Welding Of Ultra High-Strength Automotive Sheet Steel, Jack H. Sederstrom

Theses and Dissertations

Spot friction welding (SFW) was performed on ultra high strength steel (UHSS) steel sheet commonly used in automobile manufacturing. Alloys studied included DP780, DP780EG, DP980, and DF140T sheet steel of varying thickness from 1.2 mm to 1.4 mm. Welding was accomplished using a PCBN standard tool. Weld strengths were then compared to a proposed AWS standard. Initial hardness readings were taken in cross sectioned samples. Grain structure in a SFW is presented. Resistance spot welds were created in three steels. This study focuses on the strength of SFW joints as compared to traditional resistance spot welding (RSW) in welding like …

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Improving Machine Learning Through Oracle Learning, Joshua Ephraim Menke Mar 2007

Improving Machine Learning Through Oracle Learning, Joshua Ephraim Menke

Theses and Dissertations

The following dissertation presents a new paradigm for improving the training of machine learning algorithms, oracle learning. The main idea in oracle learning is that instead of training directly on a set of data, a learning model is trained to approximate a given oracle's behavior on a set of data. This can be beneficial in situations where it is easier to obtain an oracle than it is to use it at application time. It is shown that oracle learning can be applied to more effectively reduce the size of artificial neural networks, to more efficiently take advantage of domain experts …

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Ria: An Rf Interference Avoidance Algorithm For Heterogeneous Wireless Networks, Daniel P. Delorey, Qiuyi Duan, Charles D. Knutson, Manoj Pandey, Lei Wang, Ryan W. Woodings, Daniel Zappala Mar 2007

Ria: An Rf Interference Avoidance Algorithm For Heterogeneous Wireless Networks, Daniel P. Delorey, Qiuyi Duan, Charles D. Knutson, Manoj Pandey, Lei Wang, Ryan W. Woodings, Daniel Zappala

Faculty Publications

Devices with multiple wireless interfaces are becoming increasingly popular. We envision that these devices will become the building block for future mesh networks, providing seamless connectivity across a range of heterogeneous devices. Although these devices typically implement frequency sharing, using either Direct Sequence Spread Spectrum (DSSS) or Frequency Hopping Spread Spectrum (FHSS), they may still interfere with one another. In this paper we provide a novel Radio Interference Avoidance (RIA) algorithm that solves the problem of interference between IEEE 802.11 and Bluetooth. We then extend this algorithm to other types of DSSS and FHSS combinations. Though the algorithm is limited …

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Analysis Of Stacked Rotated Gratings, Gregory P. Nordin, P. C. Deguzman, J. Jiang Mar 2007

Analysis Of Stacked Rotated Gratings, Gregory P. Nordin, P. C. Deguzman, J. Jiang

Faculty Publications

We study the rigorous design and analysis of stacked rotated gratings (SRGs) for novel photonic devices. A concept of sampling frequency is proposed to systematically design SRGs. With the help of a rectangular sampling lattice, we extend the standard 3D rigorous coupled-wave analysis (RCWA) algorithm to the analysis of SRGs. The resultant SRG-RCWA algorithm can be used to exactly analyze SRGs that have grating parameters that match the Fourier expansion represented by the sampling lattice. SRGs that do not fall in this category can often still be closely approximated with our approach. The SRG-RCWA algorithm has been successfully applied to …

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Pyridinium Bis-Retinoids: Extraction, Synthesis, And Folate Coupling, Mary Allison Alvarez Mar 2007

Pyridinium Bis-Retinoids: Extraction, Synthesis, And Folate Coupling, Mary Allison Alvarez

Theses and Dissertations

This thesis is divided into two parts.Part I describes the organic extraction, separation, and liquid chromatographic-mass spectrometric analysis of chromophores from human and bovine retinal pigment epithelium. Flurorophores in the retinal pigment epithelium have been implicated in age related macular degeneration. In addition, the synthesis and characterization of a number of bis-retinoid type compounds that may potentially be found in such extracts, or that may be used for insight into pyridinium bis-retinoid reactivity, was accomplished.Part II describes a study of pyridinium bis-retinoid-folic acid coupling with respect to linker type, linker length, and nature of the linkage. Folic acid has been …

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Circuit And Modeling Solutions For High-Speed Chip-To-Chip Communication, Timothy Mowry Hollis Mar 2007

Circuit And Modeling Solutions For High-Speed Chip-To-Chip Communication, Timothy Mowry Hollis

Theses and Dissertations

This dissertation presents methods for modeling and mitigating voltage noise and timing jitter across high-speed chip-to-chip interconnects. Channel equalization and associated tuning schemes have been developed to target the distinct characteristics and signal degradation exhibited in the clock and data signals of multi-Gigabit/second digital communication links. Multiple methods for generating realistically degraded signals for the purpose of simulation are also presented and used to verify the proposed equalization and filtering topologies. Specifically, a new technique for modeling high-speed jittery clocks in the frequency domain is presented and shown to reduce transient simulation time and memory requirements, while simultaneously improving the …

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Obstacle Annotation By Demonstration, Michael David Clement Mar 2007

Obstacle Annotation By Demonstration, Michael David Clement

Theses and Dissertations

By observing human driving with a “digital head" (combined video camera and accelerometers) and taking a few hand annotations, we can automatically annotate regions in a robot's field of view that should be interpreted as obstacles to be avoided. This is accomplished by detecting the movement for a given frame in a video. Some hand annotations of video frames are necessary and they are used to create Probability Grids. Using the movement data and the Probability Grids, it is possible to annotate large amounts of video data quickly in an automated system.

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The Effect Of Birth Order On Infant Injury, Heather L. Van Duker Mar 2007

The Effect Of Birth Order On Infant Injury, Heather L. Van Duker

Theses and Dissertations

Pediatric injury is both common and expensive. Finding ways to prevent pediatric injury is a major public health concern. Many studies have investigated various aspects of pediatric injury, and some suggest that birth order may be an important risk factor for pediatric injury. This study further examined the relationship of birth order with pediatric injury, specifically studying the association of birth order with emergency department-attended infant injury while adjusting for other important family and individual covariates. Data for analysis included Utah birth certificate, death certificate, and hospital emergency department datasets, which were probabilistically linked to obtain complete demographic and injury …

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Hope For The Fatherless?: A Grounded Interpretive Approach, Anna Manja Larcher Mar 2007

Hope For The Fatherless?: A Grounded Interpretive Approach, Anna Manja Larcher

Theses and Dissertations

Psychology's literature regarding fatherlessness is not only grim, mainly pointing out the negative consequences of fatherlessness, but it also does not provide much specific information about fatherless individuals' experiences. A pilot study revealed that fatherless individuals do not always suffer from the loss of their father and that they also have the ability to overcome the negative consequences commonly associated with father loss. The research questions for this study presented themselves naturally after reviewing the literature and after considering the results of my pilot study, namely, “What do fatherless individuals actually experience in being fatherless, and what is the nature …

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Grating Lobe Reduction In Transducer Arrays Through Structural Filtering Of Supercritical Plates, Brian E. Anderson, Stephen A. Hambric, Jack W. Hughes Mar 2007

Grating Lobe Reduction In Transducer Arrays Through Structural Filtering Of Supercritical Plates, Brian E. Anderson, Stephen A. Hambric, Jack W. Hughes

Faculty Publications

The effect of placing a structural acoustic filter between water and the transducer elements of an array to help reduce undesirable grating lobes is investigated. A supercritical plate is mounted to transducer elements with a thin decoupling polyurethane layer between the transducers and the plate. The plate acts as a radiation/incidence angle filter to pass energy at angles near normal incidence, but suppress energy at large incidence angles. Grating lobe reduction is achieved at the expense of limiting the available steering of the main lobe. Within this steer angle limitation, the main lobe can be steered as normal while the …

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Observational Studies Of Software Engineering Using Data From Software Repositories, Daniel Pierce Delorey Mar 2007

Observational Studies Of Software Engineering Using Data From Software Repositories, Daniel Pierce Delorey

Theses and Dissertations

Data for empirical studies of software engineering can be difficult to obtain. Extrapolations from small controlled experiments to large development environments are tenuous and observation tends to change the behavior of the subjects. In this thesis we propose the use of data gathered from software repositories in observational studies of software engineering. We present tools we have developed to extract data from CVS repositories and the SourceForge Research Archive. We use these tools to gather data from 9,999 Open Source projects. By analyzing these data we are able to provide insights into the structure of Open Source projects. For example, …

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Development Of An H-Alpha Index For The Detection Of Pms Candidates In Young Open Clusters, Liberty Rae Evanko Mar 2007

Development Of An H-Alpha Index For The Detection Of Pms Candidates In Young Open Clusters, Liberty Rae Evanko

Theses and Dissertations

One phase of formation of medium- and low-mass stars is the optically visible phase known as the pre-main-sequence or PMS phase. In order to further the understanding of this phase, more of these PMS objects need to be identified and classified. Previous techniques have used photometry to identify possible PMS objects by their characteristic Hα emission. Once identified these objects can be studied spectroscopically yielding complete PMS classification. This study develops a method to locate these emission objects that overcomes two limitations of previous techniques. The first limitation is the need for the creation of reddening maps. It is eliminated …

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Stylized Hatching For 3d Animation, Trent Fielding Crow Mar 2007

Stylized Hatching For 3d Animation, Trent Fielding Crow

Theses and Dissertations

Much research has been done in creating non-photorealistic renderings of objects that mimic the look of hand-made drawings by traditional artists. This thesis extends work in this area by presenting an NPR hatching method that can be applied to 3D animated films to help them feel more hand drawn. In contrast to most other NPR methods, this method preserves the 3D lighting and effects of the film that make it interesting to watch. This process includes a procedural algorithm to create a hatching pattern that can be easily integrated into any film's pipeline that uses Renderman. In addition, we create …

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The Role Of Ultrasound Cavitation In Liposome Size Reduction, William G. Pitt, Eric S. Richardson, Dixon J. Woodbury Mar 2007

The Role Of Ultrasound Cavitation In Liposome Size Reduction, William G. Pitt, Eric S. Richardson, Dixon J. Woodbury

Faculty Publications

Liposome size is a vital parameter of many quantitative biophysical studies. Sonication, or exposure to ultrasound, is used widely to manufacture artificial liposomes, yet little is known about the mechanism by which liposomes are affected by ultrasound. Cavitation, or the oscillation of small gas bubbles in a pressure-varying field, has been shown to be responsible for many biophysical effects of ultrasound on cells. Collapse cavitation is manifested in the acoustic spectrum by an f/2 subharmonic and an increase in broadband noise. In this study, we attempted to correlate the presence of cavitation with a decrease in liposome size. Lipid suspensions …

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Bounds And Conditions: A Kolob In Our Solar System?, David D. Allred Mar 2007

Bounds And Conditions: A Kolob In Our Solar System?, David D. Allred

Faculty Publications

In 2003, Dialogue ran adjacent essays by two scientists, David Tolman and David Allred. The two Davids had been students together at Princeton, attending the same student ward. Decades after Princeton, Tolman had left Mormonism and Allred had stayed. Their essays are a fascinating juxtaposition. In the course of his piece, David Allred ventured for a few paragraphs into a discussion of the planet Jupiter and its role as a governor and protector in our solar system—a type of Kolob. Although the other author dismissed the topic as “fanciful physics,” my own interest was piqued. I asked Dr. Allred, who …

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Graphical And Bayesian Analysis Of Unbalanced Patient Management Data, Emily Stewart Righter Mar 2007

Graphical And Bayesian Analysis Of Unbalanced Patient Management Data, Emily Stewart Righter

Theses and Dissertations

The International Normalizing Ratio (INR) measures the speed at which blood clots. Healthy people have an INR of about one. Some people are at greater risk of blood clots and their physician prescribes a target INR range, generally 2-3. The farther a patient is above or below their prescribed range, the more dangerous their situation. A variety of point-of-care (POC) devices has been developed to monitor patients. The purpose of this research was to develop innovative graphics to help describe a highly unbalanced dataset and to carry out Bayesian analyses to determine which of five devices best manages patients. An …

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Live Surface, Christopher J. Armstrong Feb 2007

Live Surface, Christopher J. Armstrong

Theses and Dissertations

Live Surface allows users to segment and render complex surfaces from 3D image volumes at interactive (sub-second) rates using a novel, Cascading Graph Cut (CGC). Live Surface consists of two phases. (1) Preprocessing for generation of a complete 3D watershed hierarchy followed by tracking of all catchment basin surfaces. (2) User interaction in which, with each mouse movement, the 3D object is selected and rendered in real time. Real-time segmentation is ccomplished by cascading through the 3D watershed hierarchy from the top, applying graph cut successively at each level only to catchment basins bordering the segmented surface from the previous …

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A Coarse Grain Model For Dna, Thomas A. Knotts, Nitin Rathore, David C. Schwartz, Juan J. De Pablo Feb 2007

A Coarse Grain Model For Dna, Thomas A. Knotts, Nitin Rathore, David C. Schwartz, Juan J. De Pablo

Faculty Publications

Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using …

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A Coarse Grain Model For Dna, Thomas A. Knotts Iv, Nitin Rathore, David C. Schwartz, Juan J. De Pablo Feb 2007

A Coarse Grain Model For Dna, Thomas A. Knotts Iv, Nitin Rathore, David C. Schwartz, Juan J. De Pablo

Faculty Publications

Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using …

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Analysis Using Smoothing Via Penalized Splines As Implemented In Lme() In R, John R. Howell Feb 2007

Analysis Using Smoothing Via Penalized Splines As Implemented In Lme() In R, John R. Howell

Theses and Dissertations

Spline smoothers as implemented in common mixed model software provide a familiar framework for estimating semi-parametric and non-parametric models. Following a review of literature on splines and mixed models, details for implementing mixed model splines are presented. The examples use an experiment in the health sciences to demonstrate how to use mixed models to generate the smoothers. The first example takes a simple one-group case, while the second example fits an expanded model using three groups simultaneously. The second example also demonstrates how to fit confidence bands to the three-group model. The examples use mixed model software as implemented in …

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