Biostatistics Commons^™

Group And State-Specific Estimation In Animal Movement Models Using A Bayesian Approach, Anita Bhandari Sharma

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This research study investigates statistical approaches for modeling the movement patterns of white-tailed deer in Louisiana using GPS tracking data. We start by classifying the latent behavioral states using a hidden Markov model (HMM) and then integrate those inferred states into a state-dependent step selection framework to evaluate the land cover preferences. Standard HMMs, however, assume the same movement patterns for all animals, overlooking the differences due to characteristics such as sex, age, breeding season, etc.

To address this limitation, we extend the modeling framework to incorporate the group-level structure defined by similar characteristics or conditions to assess whether such …

Statistical And Machine Learning Approaches To Describe Factors Affecting Preweaning Mortality Of Piglets, Md Towfiqur Rahman, Tami M. Brown-Brandl, Gary A. Rohrer, Sudhendu R. Sharma, Vamsi Manthena, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the United States Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, …

Utilizing Markov Chains To Estimate Allele Progression Through Generations, Ronit Gandhi

Honors Program: Senior Projects (Public)

All populations display patterns in allele frequencies over time. Some alleles cease to exist, while some grow to become the norm. These frequencies can shift or stay constant based on the conditions the population lives in. If in Hardy-Weinberg equilibrium, the allele frequencies stay constant. Most populations, however, have bias from environmental factors, sexual preferences, other organisms, etc. We propose a stochastic Markov chain model to study allele progression across generations. In such a model, the allele frequencies in the next generation depend only on the frequencies in the current one.

We use this model to track a recessive allele …

Comparing Machine Learning Techniques With State-Of-The-Art Parametric Prediction Models For Predicting Soybean Traits, Susweta Ray

Department of Statistics: Dissertations, Theses, and Student Research

Soybean is a significant source of protein and oil, and also widely used as animal feed. Thus, developing lines that are superior in terms of yield, protein and oil content is important to feed the ever-growing population. As opposed to the high-cost phenotyping, genotyping is both cost and time efficient for breeders while evaluating new lines in different environments (location-year combinations) can be costly. Several Genomic prediction (GP) methods have been developed to use the marker and environment data effectively to predict the yield or other relevant phenotypic traits of crops. Our study compares a conventional GP method (GBLUP), a …

An Information Theory-Based Approach To Assessing Spatial Patterns In Complex Systems, Tarsha Eason, Wen Ching-Chuang, Shana Sundstrom, Heriberto Cabezas

School of Natural Resources: Faculty Publications

Given the intensity and frequency of environmental change, the linked and cross-scale nature of social-ecological systems, and the proliferation of big data, methods that can help synthesize complex system behavior over a geographical area are of great value. Fisher information evaluates order in data and has been established as a robust and effective tool for capturing changes in system dynamics, including the detection of regimes and regime shifts. The methods developed to compute Fisher information can accommodate multivariate data of various types and requires no a priori decisions about system drivers, making it a unique and powerful tool. However, the …

The Impact Of Truncating Data On The Predictive Ability For Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single-step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

School of Computing: Faculty Publications

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Native Insect Herbivory Limits Population Growth Rate Of A Non-Native Thistle, James O. Eckberg, Brigitte Tenhumberg, Svata M. Louda

Brigitte Tenhumberg Papers

The influence of native fauna on non-native plant population growth, size, and distribution is not well documented. Previous studies have shown that native insects associated with tall thistle (Cirsium altissimum) also feed on the leaves, stems, and flower heads of the Eurasian congener Cirsium vulgare, thus limiting individual plant performance. In this study, we tested the effects of insect herbivores on the population growth rate of C. vulgare. We experimentally initiated invasions by adding seeds at four unoccupied grassland sites in eastern Nebraska, USA, and recorded plant establishment, survival, and reproduction. Cumulative foliage and floral herbivory …

Group Testing Regression Models, Boan Zhang

Department of Statistics: Dissertations, Theses, and Student Research

Group testing, where groups of individual specimens are composited to test for the presence or absence of a disease (or some other binary characteristic), is a procedure commonly used to reduce the costs of screening a large number of individuals. Statistical research in group testing has traditionally focused on a homogeneous population, where individuals are assumed to have the same probability of having a disease. However, individuals often have different risks of positivity, so recent research has examined regression models that allow for heterogeneity among individuals within the population. This dissertation focuses on two problems involving group testing regression models. …

The Em Algorithm For Group Testing Regression Models Under Matrix Pooling, Christopher R. Bilder, Boan Zhang

Department of Statistics: Faculty Publications

No abstract provided.