Digital Commons Network^™

Current Navigation Points In Drug Diversion Law: Hidden Rocks In Shallow, Murky, Drug-Infested Waters, John J. Mulrooney Ii, Katherine E. Legel

Marquette Law Review

None

Full Issue, The Mcnair Team

McNair Scholars Research Journal

No abstract provided.

Avian Diversity, Abundance, And Nest Success Among Managed Prairies And Agricultural Plots In Oklahoma And Texas, Phillip J. Leonard, Douglas R. Wood, Wayne E. Meyer

The Prairie Naturalist

Over the last 50 years, grassland birds experienced rapid declines due to habitat loss and degradation as a result of agricultural practices. Our objective was to document the diversity, abundance, and nest success of bird communities using managed prairie and agricultural plots at the Tishomingo National Wildlife Refuge (NWR) in southern Oklahoma and Hagerman NWR in northern Texas. From April 1 to July 15, 2013–2014, point count surveys, nest searches, nest monitoring, and vegetation sampling were conducted among three habitat treatments: managed prairie, unharvested wheat, and fallow agricultural plots. Species richness values for potential nesting species were higher in managed …

Severe Drought Impacts Female Pheasant Physiology In Southwest Nebraska, Jessica A. Laskowski, Gwen C. Bachman, Joseph J. Fontaine

The Prairie Naturalist

In 2012, Nebraska experienced one of the worst droughts since the 1930s, accompanied by abnormally high temperatures. We studied the impacts of the 2012 summer drought on female ring-necked pheasant (Phasianus colchicus) body condition and baseline and stress-induced corticosterone concentrations (CORT). We hypothesized that drought conditions would reduce pheasant body condition, increase chronic stress resulting in elevated baseline CORT levels, and down-regulate pheasant stress response to acute stressors, resulting in reduced stress-induced CORT concentrations. In southwestern Nebraska, we captured female pheasants in 2012 (pre-drought) and 2013 (post-drought). Pheasants had poorer body condition after the drought. Although female CORT measures were …

Field Discrimination Of Prairie Deer Mice And White-Footed Mice Using Morphological Characteristics, Jacob L. Berl, Kelton M. Verble, Elizabeth A. Flaherty, Robert K.S. Swihart

The Prairie Naturalist

Field discrimination of prairie deer mice (Peromyscus maniculatus bairdii) and white-footed mice (P. leucopus noveboracensis) can be difficult throughout much of the central United States where they co-occur. We live-trapped prairie deer mice and white-footed mice within forested and row-crop habitats in central Indiana and used multiplex PCR with species-specific primers to positively determine species identification. We collected a suite of commonly measured external morphological traits (body weight and lengths of ear, hindfoot, tail, and body) from each captured animal. Individuals were assigned to species based on analysis of DNA; discriminant function analysis was used to …

R Teaching Column, Matthias Gehrke, Reed Davis, Norman Matloff, Paul Thompson, Tiffany Chen, Emily Watkins, Laurel Beckett

The R Journal

The revisit package, developed as a collaborative tool for scientists, also serves as a tool for teaching statistics, in a manner that can be highly motivating for students. Using either the included case studies or datasets/code provided by the instructor, students can explore several alternate paths of analysis, such as the effects of including/excluding certain variables, employing different types of statistical methodology and so on. The package includes features that help students follow modern statistical standards and avoid various statistical errors, such as “p-hacking” and lack of attention to outlier data.

Forwards Column, Stella Bollmann, Dianne Cook, Jasmine Dumas, John Fox, Julie Josse, Oliver Keyes, Carolin Strobl, Heather Turner, Rudolf Debelak

The R Journal

Forwards is a task force that was set up by the R Foundation in 2015 to address the under representation of women that has since widened its scope to encompass other under represented groups. The task force is organised as a core team comprising leaders from a number of sub-teams that focus on particular aspects:

Openebgm: An R Implementation Of The Gamma-Poisson Shrinker Data Mining Model, Travis Canida, John Ihrie

The R Journal

We introduce the R package openEBGM, an implementation of the Gamma-Poisson Shrinker (GPS) model for identifying unexpected counts in large contingency tables using an empirical Bayes approach. The Empirical Bayes Geometric Mean (EBGM) and quantile scores are obtained from the GPS model estimates. openEBGM provides for the evaluation of counts using a number of different methods, including the model-based disproportionality scores, the relative reporting ratio (RR), and the proportional reporting ratio (PRR). Data squashing for computational efficiency and stratification for confounding variable adjustment are included. Application to adverse event detection is discussed.

Partial Rank Data With The Hyper2 Package: Likelihood Functions For Generalized Bradley-Terry Models, Robin K. S Hankin

The R Journal

Here I present the hyper2 package for generalized Bradley-Terry models and give examples from two competitive situations: single scull rowing, and the competitive cooking game show Master Chef Australia. A number of natural statistical hypotheses may be tested straightforwardly using the software.

The R Journal (December 2017) 9(2): Complete Issue, The R Foundation

The R Journal

Editorial, Roger Bivand

Contributed Research Articles

anchoredDistr: A Package for the Bayesian Inversion of Geostatistical Parameters with Multi-type and Multi-scale Data, Heather Savoy, Falk Heße, and Yoram Rubin

dGAselID: An R Package for Selecting a Variable Number of Features in High Dimensional Data, Nicolae Teodor Melita and Stefan Holban

Allele Imputation and Haplotype Determination from Databases Composed of Nuclear Families, Nathan Medina-Rodríguez and Ángelo Santana

Visualization of Regression Models Using visreg, Patrick Breheny and Woodrow Burchett

fourierin: An R package to compute Fourier integrals, Guillermo Basulto-Elias, Alicia Carriquiry, Kris De Brabanter, and Daniel J. Nordman

Discrete Time Markov Chains with …

Anomalydetection: Implementation Of Augmented Network Log Anomaly Detection Procedures, Robert J. Gutierrez, Bradley C. Boehmke, Air Force Institute Of Technology, Cade M. Saie, Trevor J. Bihl

The R Journal

As the number of cyber-attacks continues to grow on a daily basis, so does the delay in threat detection. For instance, in 2015, the Office of Personnel Management discovered that approximately 21.5 million individual records of Federal employees and contractors had been stolen. On average, the time between an attack and its discovery is more than 200 days. In the case of the OPM breach, the attack had been going on for almost a year. Currently, cyber analysts inspect numerous potential incidents on a daily basis, but have neither the time nor the resources available to perform such a task. …

The Welchadf Package For Robust Hypothesis Testing In Unbalanced Multivariate Mixed Models With Heteroscedastic And Non-Normal Data, Pablo J. Villacorta

The R Journal

A new R package is presented for dealing with non-normality and variance heterogeneity of sample data when conducting hypothesis tests of main effects and interactions in mixed models. The proposal departs from an existing SAS program which implements Johansen’s general formulation of Welch-James’s statistic with approximate degrees of freedom, which makes it suitable for testing any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Improved type I error rate control is obtained using bootstrapping for calculating an empirical critical value, whereas robustness against non-normality is achieved through trimmed …

Mle.Tools: An R Package For Maximum Likelihood Bias Correction, Josmar Mazucheli, André Felipe B. Menezes, Saralees Nadarajah

The R Journal

Recently, Mazucheli (2017) uploaded the package mle.tools to CRAN. It can be used for bias corrections of maximum likelihood estimates through the methodology proposed by Cox and Snell (1968). The main function of the package, coxsnell.bc(), computes the bias corrected maximum likelihood estimates. Although in general, the bias corrected estimators may be expected to have better sampling properties than the uncorrected estimators, analytical expressions from the formula proposed by Cox and Snell (1968) are either tedious or impossible to obtain. The purpose of this paper is twofolded: to introduce the mle.tools package, especially the coxsnell.bc() function; secondly, to compare, for …

Liureg: A Comprehensive R Package For The Liu Estimation Of Linear Regression Model With Collinear Regressors, Muhammad Imdadullah, Muhammad Aslam, Saima Altaf

The R Journal

The Liu regression estimator is now a commonly used alternative to the conventional ordinary least squares estimator that avoids the adverse effects in the situations when there exists a considerable degree of multicollinearity among the regressors. There are only a few software packages available for estimation of the Liu regression coefficients, though with limited methods to estimate the Liu biasing parameter without addressing testing procedures. Our liureg package can be used to estimate the Liu regression coefficients utilizing a range of different existing biasing parameters, to test these coefficients with more than 15 Liu related statistics, and to present different …

Ider: Intrinsic Dimension Estimation With R, Hideitsu Hino

The R Journal

In many data analyses, the dimensionality of the observed data is high while its intrinsic dimension remains quite low. Estimating the intrinsic dimension of an observed dataset is an essential preliminary step for dimensionality reduction, manifold learning, and visualization. This paper introduces an R package, named ider, that implements eight intrinsic dimension estimation methods, including a recently proposed method based on a second-order expansion of a probability mass function and a generalized linear model. The usage of each function in the package is explained with datasets generated using a function that is also included in the package

Carx: An R Package To Estimate Censored Autoregressive Time Series With Exogenous Covariates, Chao Wang, Kung-Sik Chan

The R Journal

We implement in the R package carx a novel and computationally efficient quasi-likelihood method for estimating a censored autoregressive model with exogenous covariates. The proposed quasi-likelihood method reduces to maximum likelihood estimation in absence of censoring. The carx package contains many useful functions for practical data analysis with censored stochastic regression, including functions for outlier detection, model diagnostics, and prediction with censored time series data. We illustrate the capabilities of the carx package with simulations and an elaborate real data analysis.

Allele Imputation And Haplotype Determination From Databases Composed Of Nuclear Families, Nathan Medina-Rodríguez, Ángelo Santana

The R Journal

The alleHap package is designed for imputing genetic missing data and reconstruct non recombinant haplotypes from pedigree databases in a deterministic way. When genotypes of related individuals are available in a number of linked genetic markers, the program starts by identifying haplotypes compatible with the observed genotypes in those markers without missing values. If haplotypes are identified in parents or offspring, missing alleles can be imputed in subjects containing missing values. Several scenarios are analyzed: family completely genotyped, children partially genotyped and parents completely genotyped, children fully genotyped and parents containing entirely or partially missing genotypes, and founders and their …

Visualization Of Regression Models Using Visreg, Patrick Breheny, Woodrow Burchett

The R Journal

Regression models allow one to isolate the relationship between the outcome and an explanatory variable while the other variables are held constant. Here, we introduce an R package, visreg, for the convenient visualization of this relationship via short, simple function calls. In addition to estimates of this relationship, the package also provides pointwise confidence bands and partial residuals to allow assessment of variability as well as outliers and other deviations from modeling assumptions. The package provides several options for visualizing models with interactions, including lattice plots, contour plots, and both static and interactive perspective plots. The implementation of the …

Rqgis: Integrating R With Qgis For Statistical Geocomputing, Jannes Muenchow, Patrick Schratz, Alexander Brenning

The R Journal

Integrating R with Geographic Information Systems (GIS) extends R’s statistical capabilities with numerous geoprocessing and data handling tools available in a GIS. QGIS is one of the most popular open-source GIS, and it furthermore integrates other GIS programs such as the System for Automated Geoscientific Analyses (SAGA) GIS and the Geographic Resources Analysis Support System (GRASS) GIS within a single software environment. This and its QGIS Python API makes it a perfect candidate for console-based geoprocessing. By establishing an interface, the R package RQGIS makes it possible to use QGIS as a geoprocessing workhorse from within R. Compared to other …

A Tidy Data Model For Natural Language Processing Using Cleannlp, Taylor Arnold

The R Journal

Recent advances in natural language processing have produced libraries that extract low level features from a collection of raw texts. These features, known as annotations, are usually stored internally in hierarchical, tree-based data structures. This paper proposes a data model to represent annotations as a collection of normalized relational data tables optimized for exploratory data analysis and predictive modeling. The R package cleanNLP, which calls one of two state of the art NLP libraries (CoreNLP or spaCy), is presented as an implementation of this data model. It takes raw text as an input and returns a list of normalized …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.4.3

Afmtoolkit: An R Package For Automated Afm Force-Distance Curves Analysis, Rafael Benítez, Vicente J. Bolós, José-Luis Toca-Herrera

The R Journal

Atomic force microscopy (AFM) is widely used to measure molecular and colloidal inter actions as well as mechanical properties of biomaterials. In this paper the afmToolkit R package is introduced. This package allows the user to automatically batch process AFM force-distance and force-time curves. afmToolkit capabilities range from importing ASCII files and preprocessing the curves (contact point detection, baseline correction...) for finding relevant physical information, such as Young’s modulus, adhesion energies and exponential decay for force relaxation and creep experiments. This package also contains plotting, summary and feature extraction functions. The package also comes with several data sets so the …

Manlymix: An R Package For Manly Mixture Modeling, Xuwen Zhu, Volodymyr Melnykov

The R Journal

Model-based clustering is a popular technique for grouping objects based on a finite mixture model. It has countless applications in different fields of study. The R package ManlyMix implements the Manly mixture model that allows modeling skewness within data groups and performs cluster analysis. ManlyMix is a powerful diagnostics tool that is capable of conducting investigation concerning the normality of variables upon fitting of a Manly forward or backward model. Theoretical foundations as well as description of functions are provided. All features of the package are illustrated with examples in great detail. The analysis of real-life datasets demonstrates the flexibility …

Rpsftm: An R Package For Rank Preserving Structural Failure Time Models, Annabel Allison, Ian R. White, Simon Bond

The R Journal

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999).

The method is randomisation based and uses only the randomised treatment group, …

Simulating Probabilistic Long-Term Effects In Models With Temporal Dependence, Christopher Gandrud, Laron K. Williams

The R Journal

The R package pltesim calculates and depicts probabilistic long-term effects in binary models with temporal dependence variables. The package performs two tasks. First, it calculates the change in the probability of the event occurring given a change in a theoretical variable. Second, it calculates the rolling difference in the future probability of the event for two scenarios: one where the event occurred at a given time and one where the event does not occur. The package is consistent with the recent movement to depict meaningful and easy-to-interpret quantities of interest with the requisite measures of uncertainty. It is the first …

Crtgeedr: An R Package For Doubly Robust Generalized Estimating Equations Estimations In Cluster Randomized Trials With Missing Data, Melanie Prague, Rui Wang, Victor De Gruttola

The R Journal

Semi-parametric approaches based on generalized estimating equations (GEE) are widely used to analyze correlated outcomes in longitudinal settings. In this paper, we present a package CRTgeeDR developed for cluster randomized trials with missing data (CRTs). For use of inverse probability weighting to adjust for missing data in cluster randomized trials, we show that other software lead to biased estimation for non-independence working correlation structure. CRTgeeDR solves this problem. We also extend the ability of existing packages to allow augmented Doubly Robust GEEestimation (DR). Simulation studies demonstrate the consistency of estimators implemented in CRTgeeDR compared to packages such as geepack and …

Queueing: A Package For Analysis Of Queueing Networks And Models In R, Pedro Cañadilla Jiménez, Yolanda Román Montoya

The R Journal

queueing is a package that solves and provides the main performance measures for both basic Markovian queueing models and single and multiclass product-form queueing networks. It can be used both in education and for professional purposes. It provides an intuitive, straightforward wayto build queueing models using S3 methods. The package solves Markovian models of the form M/M/c/K/M/FCFS, open and closed single class Jackson networks, open and closed multiclass networks and mixed networks. Markovian models are used when both the customer inter-arrival time and the server processing time are exponentially distributed. Queueing network solvers are useful for modelling situations in which …

Investigating The Determinants And Endogenous Influences Of Environmental Reputation, Young Soo Shim

Dissertations

AN ABSTRACT OF THE DISSERTATION OF Young Soo Shim, for the Doctor of Philosophy degree in Accountancy, presented on 03/10/2017, at Southern Illinois University Carbondale. TITLE: INVESTIGATING THE DETERMINANTS AND ENDOGENOUS INFLUENES OF ENVIRONMENTAL REPUTATION MAJOR PROFESSOR: Dr. Royce D. Burnett This study investigates (1) the determinants of a firm’s environmental reputation and (2) the impact of this reputation on employee productivity and financial performance. I extend existing work in this area by focusing on both the endogenous and exogenous benefits of the reputation. The endogenous benefits refer to positive impacts of the reputation on employee morale and employee productivity, …

Jittery Gauges: Combating The Polarizing Effect Of Political Data Visualizations Through Uncertainty, Bethany Blaire Hardy

Theses and Dissertations

Since the late 1800s, public data visualizations displaying election forecasts and results—such as the red and blue map of the United State—have presented an irreparably divided country. However, on November 8, 2016, the New York Times published a data visualization on their live presidential forecast page that broke over a century of visual expectations, inspiring many to tweet reactions to what popular media has dubbed the "jittery gauges." Not surprisingly, the tweets about this unique and difficult-to-interpret display were mostly negative. This paper argues, though, that the negative feedback indicates that the gauges, while imperfect, represent an important step away …

Livy's Republic: Reconciling Republic And Princeps In Ab Urbe Condita, Joshua Stewart Mackay

Theses and Dissertations

As early as Tacitus, Livian scholarship has struggled to resolve the "Livian paradox," the conflict between Livy's support of the Roman Republic and his overt approval of Augustus, who brought about the end of the Republic. This paper addresses the paradox by attempting to place Livy's writings within their proper historical and literary context. An examination of Augustus' position during the early years of Livy's writing shows that the princeps cloaked his power within the precedent of Republican autocracy, in which imperium could be unlimited in power so long as it was limited by time. As a result, although Augustus' …