Digital Commons Network^™

Stratigrapher: Concepts For Litholog Generation In R, Sébastien Wouters, Anne-Christine Da Silva, Frédéric Boulvain, Xavier Devleeschouwer

The R Journal

The StratigrapheR package proposes new concepts for the generation of lithological logs, or lithologs, in R. The generation of lithologs in a scripting environment opens new opportunities for the processing and analysis of stratified geological data. Among the new concepts presented: new plotting and data processing methodologies, new general R functions, and computer-oriented data conventions are provided. The package structure allows for these new concepts to be further improved, which can be done independently by any R user. The current limitations of the package are highlighted, along with the limitations in R for geological data processing, to help identify the …

Elliptical Symmetry Tests In R, Slad̄Ana Babić, Christophe Ley, Marko Palangetić

The R Journal

The assumption of elliptical symmetry has an important role in many theoretical developments and applications. Hence, it is of primary importance to be able to test whether that assumption actually holds true or not. Various tests have been proposed in the literature for this problem. To the best of our knowledge, none of them has been implemented in R. This article describes the R package ellipticalsymmetry which implements several well-known tests for elliptical symmetry together with some recent tests. We demonstrate the testing procedures with a real data example.

Tramme: Mixed-Effects Transformation Models Using Template Model Builder, Bálint Tamási, Torsten Hothorn

The R Journal

Linear transformation models constitute a general family of parametric regression models for discrete and continuous responses. To accommodate correlated responses, the model is extended by incorporating mixed effects. This article presents the R package tramME, which builds on existing implementations of transformation models (mlt and tram packages) as well as Laplace approximation and automatic differentiation (using the TMB package), to calculate estimates and perform likelihood inference in mixed-effects transformation models. The resulting framework can be readily applied to a wide range of regression problems with grouped data structures.

Spnetwork: A Package For Network Kernel Density Estimation, Jeremy Gelb

The R Journal

This paper introduces the new package spNetwork that provides functions to perform Network Kernel Density Estimate analysis (NKDE). This method is an extension of the classical Kernel Density Estimate (KDE), a non parametric approach to estimate the intensity of a spatial process. More specifically, it adapts the KDE for cases when the study area is a network, constraining the location of events (such as accidents on roads, leaks in pipes, fish in rivers, etc.). We present and discuss in this paper the three main versions of NKDE: simple, discontinuous, and continuous that are implemented in spNetwork. We illustrate how to …

Spfilter: An R Package For Semiparametric Spatial Filtering With Eigenvectors In (Generalized) Linear Models, Sebastian Juhl

The R Journal

Eigenvector-based Spatial filtering constitutes a highly flexible semiparametric approach to account for spatial autocorrelation in a regression framework. It combines judiciously selected eigenvectors from a transformed connectivity matrix to construct a synthetic spatial filter and remove spatial patterns from model residuals. This article introduces the spfilteR package that provides several useful and flexible tools to estimate spatially filtered linear and generalized linear models in R. While the package features functions to identify relevant eigenvectors based on different selection criteria in an unsupervised fashion, it also helps users to perform supervised spatial filtering and to select eigenvectors based on alternative user-defined …

Bcmixed: A Package For Median Inference On Longitudinal Data With The Box–Cox Transformation, Kazushi Maruo, Ryota Ishii, Yusuke Yamaguchi, Masahiko Gosho

The R Journal

This article illustrates the use of the bcmixed package and focuses on the two main functions: bcmarg and bcmmrm. The bcmarg function provides inference results for a marginal model of a mixed effect model using the Box–Cox transformation. The bcmmrm function provides model median inferences based on the mixed effect models for repeated measures analysis using the Box–Cox transformation for longitudinal randomized clinical trials. Using the bcmmrm function, analysis results with high power and high interpretability for treatment effects can be obtained for longitudinal randomized clinical trials with skewed outcomes. Further, the bcmixed package provides summarizing and visualization tools, which …

Mgee2: An R Package For Marginal Analysis Of Longitudinal Ordinal Data With Misclassified Responses And Covariates, Yuliang Xu, Shuo Shuo Liu, Grace Y. Yi

The R Journal

Marginal methods have been widely used for analyzing longitudinal ordinal data due to their simplicity in model assumptions, robustness in inference results, and easiness in the implementation. However, they are often inapplicable in the presence of measurement errors in the variables. Under the setup of longitudinal studies with ordinal responses and covariates subject to misclassification, Chen et al. (2014) developed marginal methods for misclassification adjustments using the second-order estimating equations and proposed a two-stage estimation approach when the validation subsample is available. Parameter estimation is conducted through the Newton-Raphson algorithm, and the asymptotic distribution of the estimators is established. While …

Survidm: An R Package For Inference And Prediction In An Illness-Death Model, Gustavo Soutinho, Marta Sestelo, Luís Meira-Machado

The R Journal

Multi-state models are a useful way of describing a process in which an individual moves through a number of finite states in continuous time. The illness-death model plays a central role in the theory and practice of these models, describing the dynamics of healthy subjects who may move to an intermediate "diseased" state before entering into a terminal absorbing state. In these models, one important goal is the modeling of transition rates which is usually done by studying the relationship between covariates and disease evolution. However, biomedical researchers are also interested in reporting other interpretable results in a simple and …

Lg: An R Package For Local Gaussian Approximations, Håkon Otneim

The R Journal

The package lg for the R programming language provides implementations of recent methodological advances on applications of the local Gaussian correlation. This includes the estimation of the local Gaussian correlation itself, multivariate density estimation, conditional density estimation, various tests for independence and conditional independence, as well as a graphical module for creating dependence maps. This paper describes the lg package, its principles, and its practical use.

Analysis Of Corneal Data In R With The Rpaci Package, Darío Ramos-López, Ana D. Maldonado

The R Journal

In ophthalmology, the early detection of keratoconus is still a crucial problem. Placido disk corneal topographers are essential in clinical practice, and many indices for diagnosing corneal irregularities exist. The main goal of this work is to present the R package rPACI, providing several functions to handle and analyze corneal data. This package implements primary indices of corneal irregularity (based on geometrical properties) and compound indices built from the primary ones, either using a generalized linear model or as a Bayesian classifier using a hybrid Bayesian network and performing approximate inference. rPACI aims to make the analysis of corneal …

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

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 …

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 …

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. …

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, …

Aspergillus Section Flavi, Need For A Robust Taxonomy, Renee Arias, Valerie A. Orner, Jaime Martinez-Castillo, Victor S. Sobolev

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

In a recent letter to the editor, Houbraken et al. (23) provide a series of recommendations to the microbiological community to prevent the taxonomic misidentification of genome-sequenced fungal strains. In the era of genomics and bioinformatics, postulating that 1 nucleotide (nt) within a gene can “correctly” identify a species does not seem plausible. However, the authors of the letter call this the “calmodulin barcode,” meaning nucleotide substitutions within a 506-nt region of the calmodulin gene (1). After the evolutionarily conserved rRNA (18S rRNA, internal transcribed spacer [ITS], 28S rRNA) and RNA polymerase II (2–4) showed no differences between Aspergillus flavus …

Genetic Mapping And Qtl Analysis For Peanut Smut Resistance, Francisco J. De Blas, Cecilia I. Bruno, Renee Arias, Carolina Ballén-Taborda, Eva Mamani, Claudio Oddino, Melina Rosso, Beatriz P. Costero, Marina Bressano, Juan H. Soave, Sara J. Soave, Mario I. Buteler, J. Guillermo Seijo, Alicia Massa

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Background: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. …

The Genome Of The Stable Fly, Stomoxys Calcitrans, Reveals Potential Mechanisms Underlying Reproduction, Host Interactions, And Novel Targets For Pest Control, Pia U. Olafson, Serap Aksoy, Geoffrey M. Attardo, Greta Buckmeier, Xiaoting Chen, Craig J. Coates, Megan Davis, Justin Dykema, Scott J. Emrich, Markus Friedrich, Christopher J. Holmes, Panagiotis Ioannidis, Evan N. Jansen, Emily C. Jennings, Daniel Lawson, Ellen O. Martinson, Gareth L. Maslen, Richard P. Meisel, Terence D. Murphy, Dana Nayduch, David R. Nelson, Kennan J. Oyen, Tyler J. Raszick, José M.C. Ribeiro, Hugh M. Robertson, Andrew J. Rosendale, Timothy B. Sackton, Perot Saelao, Sonja L. Swiger, Sing Hoi Sze, Aaron M. Tarone, David B. Taylor, Wesley C. Warren, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Richard K. Wilson, Evgeny M. Zdobnov, Joshua B. Benoit

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were …

Continuous Turbidity Data Used To Compute Constituent Concentrations In The South Loup River, Nebraska, 2017–18, David L. Rus, Brenda K. Densmore

United States Geological Survey: Water Reports and Publications

The South Loup River in central Nebraska has been impaired by bacteria since at least 2004, which has resulted in the river not meeting its intended use as a recreational waterway. As part of a strategy for reducing the bacterial load in the river, the United States Geological Survey (USGS), in cooperation with the Lower Loup Natural Resources District, made continuous estimates of Escherichia coli (E. coli) and nutrient concentrations during seasonal monitoring at the South Loup River at Saint Michael, Nebraska, during 2017–18. Continuous turbidity data were collected from mid-April through October in 2017 and 2018 …

Students' Definitions Of Academic Success, Brent Kelderman

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

Academic success has not been well defined consistently, and when definitions have been proposed (e.g. Kuh, Kinzie, Buckley, Bridges, & Hayek, 2006 ; York, Gibson, & Rankin, 2015), they are not always measured consistently. Is it good grades (Parker, Summerfeldt, Hogan, & Majeski, 2004), and if so, what constitutes a good grade and what should be graded? Is it understanding the material, and if so, is understanding shown by simply completing the academic tasks (Choi, 2005)? Is it perseverance and grit (Tang, Wang, Guo, & Salmela-Aro, 2019), and if so, why do many other definitions and views focus so much …

The Role Of The Next Generation Science Standards In Teachers' Curricular Choices In The Life Science Classroom, Amy Tankersley

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

In 2013 a group of experts used A Framework for K-12 Science Education (NRC, 2012) to draft the Next Generation Science Standards (NGSS), which aims to increase science literacy through integrating the concepts and practices of science into comprehensive standards for science (NGSS Lead States, 2013). As students learn to explore the content and practices of scientists, ideally, they should increase their ability to think and reason in ways that will benefit their ability to participate in society. Because of the complex nature of systematic education reform, teachers need to put significant time into implementing NGSS to fulfill the goals …

Detecting And Evaluating Cracks On Aging Concrete Members With Deep Convolutional Neural Networks, Brendan Barnes

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Cracks in concrete structures are evaluated through a timely and subjective manual inspection. The location of cracks is often recorded in an inspection report where some cracks are measured. Although measurements or locations may not be necessary for all cracks observed in concrete members, if quantitative data can be gathered in an autonomous way, allowing measurement data to be used in tracking changes in spatial and temporal scales, this quantitative data can provide useful information not yet captured in the manual inspection process. This thesis aims to construct an image-based crack detection and evaluation pipeline that can assist health monitoring …

Livestock Grazing Impacts On Crop And Soil Responses For Two Cropping Systems, Alyssa Kuhn

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Diversified crop, forage, and livestock systems are assumed to be more sustainable and economically competitive than traditional cropping systems. Objectives of this study were to determine effects of integrating grazing livestock into corn (Zea mays)-soybean (Glycine max (L.) Merr.) (C-S) and corn-soybean-wheat (Triticum aestivum L.) (C-S-W) cropping systems on plant population, grain yield, soil nutrients and soil carbon dioxide (CO₂) flux following winter grazing corn residue (both systems) and an oat (Avena sativa) cover crop (C-S-W only) planted after wheat. For the 2019 and 2020 production seasons, neither corn nor soybean plant …

The Importance Of Acquisition Learning On Nicotine And Varenicline Drug Substitution In A Drug-Discriminated Goal-Tracking Task, Brady M. Thompson, Scott T. Barrett, Y. Wendy Huynh, David A. Kwan, Jennifer E. Murray, Rick A. Bevins

Department of Psychology: Faculty Publications

Nicotine and varenicline (Chantix®; the leading non-nicotine cessation pharmacotherapy) can come to control appetitive behaviors such as goal-tracking. We tested rats (N = 48) in a drug-discriminated goal-tracking (DGT) task where each rat received daily subcutaneous injections of either nicotine (0.4 mg/kg) or saline (0.9% [w/v]) interspersed across the acquisition phase (Phase 1). On saline days, sucrose was intermittently available. On nicotine days, sucrose was withheld. All rats acquired the discrimination with increased goal-tracking rates on saline days relative to nicotine days. Following acquisition, rats were separated into four groups to assess drug-substitution and discrimination reversal in Phase 2. The …

Statistical Mediation Analysis In Regression Discontinuity Design For Causal Inference, Donna Chen

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Regression discontinuity designs (RDDs) are the most robust quasi-experimental design, but current statistical models are limited to estimates for the simple causal relationship between only two variables: the independent and dependent variables. In practice, intervening variables (or mediators) are often observed as part of the causal chain. Mediators explain the why and how a treatment or intervention works. Therefore, mediation and RDD analysis combined can be a useful tool in identifying key components or processes that make intervention programs effective while making causal inferences for improving student achievement, despite natural constraints, limitations, and ethical considerations. Without an integrated framework of …

Current Literacy Interventions For Aac Users, Payton Proud

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Purpose: Literacy provides individuals who use augmentative and alternative communication (AAC) with an avenue to share their original thoughts through generative communication. There is limited research regarding literacy intervention for AAC users, particularly in high school. This study sought to (a) identify literacy interventions used with high school AAC users, (b) determine the importance placed on literacy by SLPs for high school AAC users, and (c) compare the importance of literacy intervention in high school to other ages of AAC users and other areas of intervention.

Method: Ninety-two Nebraska school-based speech-language pathologists (SLPs) completed an online survey to answer the …

The Impact Of Beneficial Organisms In Corn Agroecosystems, Callie Rosalind Braley

Doctor of Plant Health Program: Dissertations and Student Research

Corn is one of the world’s, and Nebraska’s, most important crops. Millions of acres are planted to corn each year in the Cornhusker State. However, each year there are a plethora of arthropod, weed, and microorganism pests that rob farmers of reaching their maximum yield potential. There are many options available to manage these pests in corn agroecosystems, but one option is often underutilized: beneficial organisms. For each pest, there are a variety of natural enemies that can assist in mitigating the damage caused by pests.

Many beneficial organisms exist, and they can be grouped by the type of pest …

Examination Of Cajeput Oil (Melaleuca Cajuputi) Phytochemicals As Tools To Manage The Yellow Fever Mosquito (Aedes Aegypti L.), Ellis Johnson

Department of Entomology: Dissertations, Theses, and Student Research

The yellow fever mosquito, Aedes aegypti L., is among the most important insects as it pertains to public health. It vectors several health-endangering pathogens, including yellow fever, dengue fever, chikungunya, and Zika viruses. Insecticides are among the most effective tools used to manage mosquito populations however, their efficacy to manage mosquito populations is being threatened by insecticide resistance. This ongoing threat warrants new chemical strategies to reduce or incapacitate a mosquito population capable of pathogen transmission. Plant essential oils are candidates for identifying novel management tools for disease-vectoring arthropods. Commercially, essential oils have been used for pharmaceuticals, flavoring, fragrances, cosmetics, …

Evidence Of Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Field-Evolved Resistance To Cry3bb1 + Cry34/35ab1 Maize In Nebraska, Jordan Reinders, Emily E. Reinders, Emily Robinson, Brian W. French, Lance J. Meinke

Department of Entomology: Faculty Publications

BACKGROUND: Western corn rootworm (WCR; Diabrotica virgifera virgifera) field-evolved resistance to transgenic maize expressing the Cry3Bb1 protein derived from Bacillus thuringiensis (Bt) has been confirmed across the United States Corn Belt. Although use of pyramided hybrids expressing Cry3Bb1 + Cry34/35Ab1 has increased in recent years to mitigate existing WCR Bt resistance, susceptibility of Nebraska WCR populations to this rootworm–Bt pyramid has not been assessed. Plant-based bioassays were used to characterize the susceptibility of WCR populations to Cry3Bb1 and Cry3Bb1 + Cry34/35Ab1 maize. Populations were collected from areas of northeastern Nebraska with a history of planting Bt maize that expressed Cry3Bb1 …

Evaluation Of A Novel Approach For Assessing Biological Activity In Agricultural Soils, Karla Melgar

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Soil health is a key factor impacting soil resilience and fertility in crop production systems. Favorable soil physical and biological conditions facilitate plant nutrient absorption and nutrient cycling. Demonstrating to farmers the impacts and changes in soil biological activity under different soil management practices has been a challenge due to the limited availability of inexpensive tools for quantifying this component of soil health. The primary goal of this study was to present a simple and readily accessible tool for evaluating soil biological activity to promote the use of organic amendments in crop fields. Research plots were established in two studies …