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2021

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News From The Forwards Taskforce, Heather Turner Dec 2021

News From The Forwards Taskforce, Heather Turner

The R Journal

Forwards is an R Foundation taskforce working to widen the participation of underrepresented groups in the R project and in related activities, such as the useR! conference. This report rounds up activities of the taskforce during the second half of 2022.

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Drhotnet: An R Package For Detecting Differential Risk Hotspots On A Linear Network, Álvaro Briz-Redón, Francisco Martínez-Ruiz, Francisco Montes Dec 2021

Drhotnet: An R Package For Detecting Differential Risk Hotspots On A Linear Network, Álvaro Briz-Redón, Francisco Martínez-Ruiz, Francisco Montes

The R Journal

One of the most common applications of spatial data analysis is detecting zones, at a certain scale, where a point-referenced event under study is especially concentrated. The detection of such zones, which are usually referred to as hotspots, is essential in certain fields such as criminology, epidemiology, or traffic safety. Traditionally, hotspot detection procedures have been developed over areal units of analysis. Although working at this spatial scale can be suitable enough for many research or practical purposes, detecting hotspots at a more accurate level (for instance, at the road segment level) may be more convenient sometimes. Furthermore, it is …

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We Need Trustworthy R Packages, William Michael Landau Dec 2021

We Need Trustworthy R Packages, William Michael Landau

The R Journal

There is a need for rigorous software engineering in R packages, and there is a need for new research to bridge scientific computing with more traditional computing. Automated tools, interdisciplinary graduate courses, code reviews, and a welcoming developer community will continue to democratize best practices. Democratized software engineering will improve the quality, correctness, and integrity of scientific software, and by extension, the disciplines that rely on it

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A Guided Tour Of Bayesian Regression, Andrés Ramírez–Hassan, Mateo Graciano-Londoño Dec 2021

A Guided Tour Of Bayesian Regression, Andrés Ramírez–Hassan, Mateo Graciano-Londoño

The R Journal

This paper presents a Graphical User Interface (GUI) to carry out a Bayesian regression analysis in a very friendly environment without any programming skills (drag and drop). This paper is designed for teaching and applied purposes at an introductory level. Our GUI is based on an interactive web application using shiny and libraries from R. We carry out some applications to highlight the potential of our GUI for applied researchers and practitioners. In addition, the Help option in the main tap panel has an extended version of this paper, where we present the basic theory underlying all regression models that …

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Visual Diagnostics For Constrained Optimisation With Application To Guided Tours, H Sherry Zhang, Dianne Cook, Ursula Laa, Nicolas Langrené, Patricia Menéndez Dec 2021

Visual Diagnostics For Constrained Optimisation With Application To Guided Tours, H Sherry Zhang, Dianne Cook, Ursula Laa, Nicolas Langrené, Patricia Menéndez

The R Journal

A guided tour helps to visualise high-dimensional data by showing low-dimensional projections along a projection pursuit optimisation path. Projection pursuit is a generalisation of principal component analysis in the sense that different indexes are used to define the interestingness of the projected data. While much work has been done in developing new indexes in the literature, less has been done on understanding the optimisation. Index functions can be noisy, might have multiple local maxima as well as an optimal maximum, and are constrained to generate orthonormal projection frames, which complicates the optimization. In addition, projection pursuit is primarily used for …

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A Unifying Framework For Parallel And Distributed Processing In R Using Futures, Henrik Bengtsson Dec 2021

A Unifying Framework For Parallel And Distributed Processing In R Using Futures, Henrik Bengtsson

The R Journal

A future is a programming construct designed for concurrent and asynchronous evaluation of code, making it particularly useful for parallel processing. The future package implements the Future API for programming with futures in R. This minimal API provides sufficient constructs for implementing parallel versions of well-established, high-level map-reduce APIs. The future ecosystem supports exception handling, output and condition relaying, parallel random number generation, and automatic identification of globals lowering the threshold to parallelize code. The Future API bridges parallel frontends with parallel backends, following the philosophy that end-users are the ones who choose the parallel backend while the developer focuses …

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Compmodels: A Suite Of Computer Model Test Functions For Bayesian Optimization, Tony Pourmohamad Dec 2021

Compmodels: A Suite Of Computer Model Test Functions For Bayesian Optimization, Tony Pourmohamad

The R Journal

The CompModels package for R provides a suite of computer model test functions that can be used for computer model prediction/emulation, uncertainty quantification, and calibration. Moreover, the CompModels package is especially well suited for the sequential optimization of computer models. The package is a mix of real-world physics problems, known mathematical functions, and black-box functions that have been converted into computer models with the goal of Bayesian (i.e., sequential) optimization in mind. Likewise, the package contains computer models that represent either the constrained or unconstrained optimization case, each with varying levels of difficulty. In this paper, we illustrate the use …

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Generalized Linear Randomized Response Modeling Using Glmmrr, Jean-Paul Fox, Konrad Klotzke, Duco Veen Dec 2021

Generalized Linear Randomized Response Modeling Using Glmmrr, Jean-Paul Fox, Konrad Klotzke, Duco Veen

The R Journal

Randomized response (RR) designs are used to collect response data about sensitive behaviors (e.g., criminal behavior, sexual desires). The modeling of RR data is more complex since it requires a description of the RR process. For the class of generalized linear mixed models (GLMMs), the RR process can be represented by an adjusted link function, which relates the expected RR to the linear predictor for most common RR designs. The package GLMMRR includes modified link functions for four different cumulative distributions (i.e., logistic, cumulative normal, Gumbel, Cauchy) for GLMs and GLMMs, where the package lme4 facilitates ML and REML estimation. …

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Passo: An R Package For Assessing Partial Association Between Ordinal Variables, Shaobo Li, Xiaorui Zhu, Yuejie Chen, Dungang Liu Dec 2021

Passo: An R Package For Assessing Partial Association Between Ordinal Variables, Shaobo Li, Xiaorui Zhu, Yuejie Chen, Dungang Liu

The R Journal

Partial association, the dependency between variables after adjusting for a set of covariates, is an important statistical notion for scientific research. However, if the variables of interest are ordered categorical data, the development of statistical methods and software for assessing their partial association is limited. Following the framework established by Liu et al. (2021), we develop an R package PAsso for assessing Partial Associations between ordinal variables. The package provides various functions that allow users to perform a wide spectrum of assessments, including quantification, visualization, and hypothesis testing. In this paper, we discuss the implementation of PAsso in …

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An R Package For Non-Normal Multivariate Distributions: Simulation And Probability Calculations From Multivariate Lomax (Pareto Type Ii) And Other Related Distributions, Zhixin Lun, Ravindra Khattree Dec 2021

An R Package For Non-Normal Multivariate Distributions: Simulation And Probability Calculations From Multivariate Lomax (Pareto Type Ii) And Other Related Distributions, Zhixin Lun, Ravindra Khattree

The R Journal

Convenient and easy-to-use programs are readily available in R to simulate data from and probability calculations for several common multivariate distributions such as normal and t. However, functions for doing so from other less common multivariate distributions, especially those which are asymmetric, are not as readily available, either in R or otherwise. We introduce the R package NonNorMvtDist to generate random numbers from multivariate Lomax distribution, which constitutes a very flexible family of skewed multivariate distributions. Further, by applying certain useful properties of multivariate Lomax distribution, multivariate cases of generalized Lomax, Mardia’s Pareto of Type I, Logistic, Burr, Cook-Johnson’s uniform, …

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Decay Of Correlations For Weakly Expanding Dynamical Systems With Dini Potentials Under Optimal Quasi-Gap Condition, Yunping Jiang, Yuan-Ling Ye Dec 2021

Decay Of Correlations For Weakly Expanding Dynamical Systems With Dini Potentials Under Optimal Quasi-Gap Condition, Yunping Jiang, Yuan-Ling Ye

Publications and Research

We find an optimal quasi-gap condition for a weakly expanding dynamical system associated with Dini potential. Under this optimal quasi-gap condition, we prove the Ruelle operator theorem and further the decay of the correlations for any weakly expanding dynamical systems with Dini potentials.

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Virtual And Blended Instruction And School Lunch Eligibility On Student Achievement During The Coronavirus Pandemic, Leann Ferrell Helms Dec 2021

Virtual And Blended Instruction And School Lunch Eligibility On Student Achievement During The Coronavirus Pandemic, Leann Ferrell Helms

College of Education Dissertations

The purpose of this dissertation was to determine the effects of virtual and blended instruction and school lunch eligibility on student achievement during the coronavirus (COVID-19) pandemic measured by the 2021 ACT Aspire Interim Assessment scores. Scores chosen were from seventh- and ninth-grade students in five schools giving the ACT Aspire Interim Assessment prior to Winter Break. The scores were used to provide academic performance data for the dependent variables used in each hypothesis. Bronfenbrenner developed the ecological systems theory in 1979 to identify environmental factors affecting a person’s characteristics over a lifetime. COVID-19 affected education and instructional delivery during …

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Gpu-Based Monte Carlo Applications In Radiation Medicine, Youfang Lai Dec 2021

Gpu-Based Monte Carlo Applications In Radiation Medicine, Youfang Lai

Physics Dissertations - Archive

Radiation can be used to image tumor site or kill tumor cells noninvasively, playing an important role in tumor diagnosis and treatment. Because of the increasing burden that cancer brings to the society, there always exists the demand of improving imaging resolution and contrast and improving radiation conformity for therapy. This depends on not only the advances of techniques, but, probably more importantly, the accurate and efficient modelling of radiation transport, enabling research on proof-of-concept for new tech and more complicated physics and chemical process in a quantitative way. Monte Carlo (MC) simulation method has been extensively used in medical …

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Art Education As Mutual Aid: Community And Social Justice Based Initiatives, Janelle O'Malley Dec 2021

Art Education As Mutual Aid: Community And Social Justice Based Initiatives, Janelle O'Malley

Student Projects

In the wake of the COVID-19 pandemic, education has drastically changed. The months of pandemic coupled with rising political upheaval left issues with schooling at the bottom of the list. Yet, the repercussions of the pandemic have forever changed the face of our educational system. Especially hard hit during this time was subjects deemed unimportant such as music and art. These classes, which already have faced their fair amount of cutbacks, were once again left on the chopping block. Even though the Every Student Succeeds Act (ESSA) in 2015 ensured that art would be treated as a core subject, it …

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Understanding Students’ Global Interdependence In Science Instruction, Walter S. Smith Dec 2021

Understanding Students’ Global Interdependence In Science Instruction, Walter S. Smith

Journal of Global Education and Research

Multiple American educational organizations such as the National Education Association, Association for Supervision and Curriculum Development, and the Council of Chief State School Officers have advocated for globalizing the K-12 curriculum. The National Science Teaching Association (NSTA) in a position statement on international education and the Next Generation Science Standards have produced goals and standards for internationalizing the science curriculum by addressing topics such as climate change, environment, and disease that cross borders. In contrast to those pronouncements on the curriculum, this article views global science education through an instructional lens that focuses on a students’ global interdependence in science …

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Energy Dissipation During Geomagnetic Storms, Fatemeh Bagheri Dec 2021

Energy Dissipation During Geomagnetic Storms, Fatemeh Bagheri

Physics Dissertations - Archive

Some fraction of the solar wind energy is transferred to the Earth magnetosphere and ionosphere. Sometimes this transfer of energy is exceptionally large, producing a magnetic storm. Storms occur when the Interplanetary Magnetic Field (IMF) turns southward and remains southward for an extended period of time. During the main phase of many magnetic storms, the solar wind Mach number is low, and IMF magnitude is large. Under these conditions, the ionospheric potential saturates, and it becomes relatively insensitive to further increases in the IMF magnitude. On the other hand, the dayside merging rate and the potential become sensitive to the …

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The Arecibo Observatory As An Instrument For Investigating Orbital Debris, James Isaiah Murray Dec 2021

The Arecibo Observatory As An Instrument For Investigating Orbital Debris, James Isaiah Murray

Physics Dissertations - Archive

In this dissertation, the Arecibo Observatory, both past and future, as an instrument for investigating orbital debris is investigated. For over three decades, models of the orbital debris environment in low Earth orbit (LEO) have been developed to assess the risk posed by orbital debris to spacecraft. While terrestrial radar measures debris 3 mm and larger and in-situ measurements provide data for debris smaller than 1 mm, no good data sources exist for debris between 1 mm and 3 mm in size. This results in large variations between competing orbital debris models. It also happens to be the size regime …

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Electronic And Magnetic Properties Of Metal Doped Silicon-Carbide Fullerene-Type Nanostructures, Hussain Jabreel Alathlawi Dec 2021

Electronic And Magnetic Properties Of Metal Doped Silicon-Carbide Fullerene-Type Nanostructures, Hussain Jabreel Alathlawi

Physics Dissertations - Archive

Silicon carbide (SiC) is a technologically significant material. A recent report on the abundance of C60 fullerenes in interstellar space, along with the presence of SiC precursors, sparked interest in potentially similar SiC nanostructures. C60 and C70 fullerenes were found experimentally and are an exceptionally stable form of carbon. As Si and C have similar valence electron configurations, it has been long envisioned that Si and SiC could also form similar fullerene-type structures. In this dissertation, Si30C30 fullerene-derived clusters were studied from the first principles theory, starting from an ideal Si60 fullerene template with various arrangements of silicon and carbon …

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Nonlinear Mode Coupling Coefficients In Extrasolar Hot Jupiter Systems With Non-Solar Type Host Stars, Niyousha Davachi Dec 2021

Nonlinear Mode Coupling Coefficients In Extrasolar Hot Jupiter Systems With Non-Solar Type Host Stars, Niyousha Davachi

Physics Theses - Archive

Short period planets tidally excite internal gravity modes within their host star. These excited modes, known collectively as the dynamical tide, dissipate orbital energy and cause the planet’s orbit to decay. In hot Jupiter systems, resonantly excited gmodes are driven to such large amplitudes in the stellar core that they nonlinearly excite a sea of secondary modes. These secondary modes can greatly enhance the efficiency of tidal dissipation compared to linear theory predictions and thus significantly increase the rate of orbital decay. In this thesis we calculate the three-mode coupling coefficients between the excited g-modes of hot Jupiter host stars. …

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Distributed Estimation And Inverse Reinforcement Learning For Multi-Agent Systems, Bosen Lian Dec 2021

Distributed Estimation And Inverse Reinforcement Learning For Multi-Agent Systems, Bosen Lian

Electrical Engineering Dissertations - Archive

Consensus-based distributed Kalman filters for estimation with multiple targets have attracted considerable attention. Most of the existing Kalman filters use the average consensus approach, which tends to have a low convergence speed. They also rarely consider the impacts of limited sensing range and target mobility on the information flow topology. The robustness properties, i.e., gain margins and phase margins of distributed Kalman filtering algorithms are still open problems. In the interactions of controlled dynamical agents, it is often assumed that the agents are "rational" in the sense of attempting to act in such a way as to optimize some prescribed …

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Fast And Parallelizable Numerical Algorithms For Large Scale Conic Optimization Problems, Muhammad Adil Dec 2021

Fast And Parallelizable Numerical Algorithms For Large Scale Conic Optimization Problems, Muhammad Adil

Electrical Engineering Dissertations - Archive

Many real world problems from various application areas such as engineering, finance and operation research can be cast as optimization problems. Generally, the goal is to optimize an objective function under a set of constraints. Traditionally, convex optimization problems are solved by an interior point method (IPM). Interior point methods proved to achieve high accuracy for moderate size problems. However, the computation cost of iterations of these iterative algorithms grows non-linearly with the dimension of the problem. Although interior-point methods are robust and theoretically sound, they do not scale well for very large conic optimization programs. Computational cost, memory issues, …

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Headspace-Solid Phase Micro Extraction – Gas Chromatography – Mass Spectrometry (Hs-Spme-Gc-Ms) Analysis For Oak Barrel Flavor Compounds In Whiskey, Hailey F. Jarzynka Dec 2021

Headspace-Solid Phase Micro Extraction – Gas Chromatography – Mass Spectrometry (Hs-Spme-Gc-Ms) Analysis For Oak Barrel Flavor Compounds In Whiskey, Hailey F. Jarzynka

Chemistry & Biochemistry Theses - Archive

This study presents a method to simultaneously detect both fault compounds and oak barrel flavor compounds in whiskey using headspace-solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). A major contaminant in whiskey is geosmin and an array of oak barrel compounds includes 2-methoxy-4-methylphenol, 5-methylfurfural, guaiacol, trans-whiskey lactone, 2-methoxy-4-vinylphenol, 4-ethylguaiacol, eugenol, vanillin, and 4-ethylphenol. Geosmin is a fault compound that produces a musty or moldy taste to the whiskey and the other compounds originate from the barrels in which the whiskey is aged in and transfer to the whiskey in the aging process. Each compound was quantitated and 15 different whiskies were compared …

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Comparative Assessment Of Different Optimization Techniques For Turning Operations., Samar Elsanabary, Ahmed Elkaseer, Saber Abd-Rabbo, Mohamed Ali, Shabaan Abdou Dec 2021

Comparative Assessment Of Different Optimization Techniques For Turning Operations., Samar Elsanabary, Ahmed Elkaseer, Saber Abd-Rabbo, Mohamed Ali, Shabaan Abdou

Mansoura Engineering Journal

This paper presents a comparative study that was conducted aiming at evaluating three different optimization techniques; namely, linguistic Fuzzy Logic Control (FLC), Sequential Quadratic Programming (SQP), and the Bees Algorithm. Initially, a well-constructed deterministic model of the turning operation was utilized to feed two optimization techniques, (SQP) and the Bees Algorithm. The results were assessed and compared with those already obtained using (FLC) method that was published in the literature. The study outcomes revealed that, although The Bees Algorithm gave acceptable output, the (SQP) technique identified the optimal cutting conditions. As a result, one can argue that the (SQP) is …

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3-In-1 Medical Lancet, Jonathan J. Panella, Gage Vogtlin, Marissa Koski, Benjamin Neyland Dec 2021

3-In-1 Medical Lancet, Jonathan J. Panella, Gage Vogtlin, Marissa Koski, Benjamin Neyland

Mechanical Engineering

First responders need a quick, sterile, and convenient way to sample blood for glucose testing because glucose levels are a vital metric in assessing time-critical emergency situations. The blood sampling process consists of pre-sterilizing the sample site on the skin with an alcohol pad, pricking the skin with a lancet, and lastly, after sampling, putting a bandage over the prick site. The scope of this project is to design a device which integrates and streamlines the use of the three sub-processes (sterilization, lancing, and bandaging) while upholding the necessary requirements of a single-use medical device and considering other factors which …

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Essential Programs And Services Report Of Findings: Gifted & Talented Education, Lisa Morris Phd, Amy F. Johnson Phd Dec 2021

Essential Programs And Services Report Of Findings: Gifted & Talented Education, Lisa Morris Phd, Amy F. Johnson Phd

Gifted & Talented

This review of the Gifted and Talented (G&T) funding component within the Essential Programs and Services (EPS) education cost model begins with a summary of our most recent (2019) analyses of the G&T funding patterns and trends in Maine. Next we provide updated data (Part I) about G&T program implementation and enrollment in Maine public schools in FY2020 and FY2021 to confirm that trends from prior studies persist. We then provide a summary of the available research literature on the rationale and effectiveness of G&T programming in order to revisit the underlying tenets of this aspect of Maine’s funding model …

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Soil Structure And Soil Moisture Dynamics Inferred From Time-Lapse Electrical Resistivity Tomography, Travis Nielson, John Bradford, Jen Pierce, Mark Seyfried Dec 2021

Soil Structure And Soil Moisture Dynamics Inferred From Time-Lapse Electrical Resistivity Tomography, Travis Nielson, John Bradford, Jen Pierce, Mark Seyfried

Geosciences Faculty Publications and Presentations

The semi-arid sagebrush steppe in the western United States faces pressures from the agriculture industry, recreation use, invasive grasses, and a changing climate. A key to facilitating the healthy management of this ecosystem is understanding the distribution and behavior of soil moisture in the vadose zone in both natural and agricultural settings. Within unsaturated environments, soil moisture is spatially and temporally heterogeneous, and changes in porosity and permeability within arid soils complicate characterization of soil hydrologic properties. Importantly, accumulations of ‘caliche’ or pedogenic calcium carbonate in arid soils can greatly limit permeability; however, observing the role that caliche plays in …

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Comparison Of Different Analytical Strategies For Classifying Invasive Wetland Vegetation In Imagery From Unpiloted Aerial Systems (Uas), Louis Will Jochems, Jodi Brandt, Andrew Monks, Megan Cattau, Nicholas Kolarik, Jason Tallant, Shane Lishawa Dec 2021

Comparison Of Different Analytical Strategies For Classifying Invasive Wetland Vegetation In Imagery From Unpiloted Aerial Systems (Uas), Louis Will Jochems, Jodi Brandt, Andrew Monks, Megan Cattau, Nicholas Kolarik, Jason Tallant, Shane Lishawa

Human-Environment Systems Research Center Faculty Publications and Presentations

Detecting newly established invasive plants is key to prevent further spread. Traditional field surveys are challenging and often insufficient to identify the presence and extent of invasions. This is particularly true for wetland ecosystems because of difficult access, and because floating and submergent plants may go undetected in the understory of emergent plants. Unpiloted aerial systems (UAS) have the potential to revolutionize how we monitor invasive vegetation in wetlands, but key components of the data collection and analysis workflow have not been defined. In this study, we conducted a rigorous comparison of different methodologies for mapping invasive Emergent (Typha …

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Reproductive Success Of Captive-Reared Allegheny Woodrats (Neotoma Magister) Released Into Genetically Depauperate Populations, Miracle M. Davis, Timothy J. Smyser, Scott A. Johnson, Joseph Duchamp, Jeffery L. Larkin, Robert K. Swihart, Jacqueline M. Doyle Dec 2021

Reproductive Success Of Captive-Reared Allegheny Woodrats (Neotoma Magister) Released Into Genetically Depauperate Populations, Miracle M. Davis, Timothy J. Smyser, Scott A. Johnson, Joseph Duchamp, Jeffery L. Larkin, Robert K. Swihart, Jacqueline M. Doyle

United States Department of Agriculture Wildlife Services: Staff Publications

Habitat fragmentation and degradation have led to a proliferation of small and isolated populations that are vulnerable to genetic erosion. Reduction in habitat and concomitant declines in population connectivity can expediate the collapse of species that exist as natural metapopulations. In recent years, Allegheny woodrats (Neotoma magister) have experienced local extirpations and declines in genetic diversity across their range due to disease-related mortality, reduced food availability, and disruption of connectivity among subpopulations. In response, we developed a captive-breeding program to facilitate genetic management of isolated woodrat populations in Indiana. Between 2010 and 2012, 27 captive-reared individuals were released to four …

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Experimental Measurement Of Sharp Thz Absorption Signatures From Nucleic Acid Solutions In Nanofluidic Channels, Elliott R. Brown, Edgar A. Mendoza Dec 2021

Experimental Measurement Of Sharp Thz Absorption Signatures From Nucleic Acid Solutions In Nanofluidic Channels, Elliott R. Brown, Edgar A. Mendoza

Physics Faculty Publications

We report on the room-temperature experimental measurement of THz absorption signatures in aqueous, double-stranded nucleic acid solutions confined to the submicron silica channels on fused quartz substrates using THz frequency-domain (photomixing) spectroscopy. Three sharp (i.e., strong and narrow) signatures, ~10–20 GHz FWHM, are observed in the shortest base pair sample—small interfering, double-stranded (ds) RNA—in the range of 800 GHz to 1.1 THz. Three similar signatures are also observed in a 50-bp dsDNA ladder sample. For a 1-kbp dsDNA ladder sample, the three are still evident, but are broadened and weakened. For a 48.5-kbp sample (λ-DNA), no prominent signatures are observed, …

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Sensor-Based Prediction Of Mental Effort During Learning From Physiological Data: A Longitudinal Case Study, Ankita Agarwal, Josephine Graft, Noah Schroeder, William Romine Dec 2021

Sensor-Based Prediction Of Mental Effort During Learning From Physiological Data: A Longitudinal Case Study, Ankita Agarwal, Josephine Graft, Noah Schroeder, William Romine

Biological Sciences Faculty Publications

Trackers for activity and physical fitness have become ubiquitous. Although recent work has demonstrated significant relationships between mental effort and physiological data such as skin temperature, heart rate, and electrodermal activity, we have yet to demonstrate their efficacy for the forecasting of mental effort such that a useful mental effort tracker can be developed. Given prior difficulty in extracting relationships between mental effort and physiological responses that are repeatable across individuals, we make the case that fusing self-report measures with physiological data within an internet or smartphone application may provide an effective method for training a useful mental effort tracking …

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