Digital Commons Network^™

Notes: Examining The Potential Competitive Effects Of Ventenata Dubia On Annual And Perennial Grasses, Shawn Mckay, Lesley R. Morris, Christopher E. Morris, Elizabeth A. Leger

The Prairie Naturalist

Portions of the United States are becoming increasingly dominated by annual species, with cheatgrass (Bromus tectorum L.) and medusahead (Taeniatherum caput-medusae [L.] Nevski) as the most common and well-known invaders (Bansal et al. 2014). Other invasive annual species also are present and increasing in abundance, including ventenata (Ventenata dubia [Leers] Coss.), an invasive annual grass that has been expanding within the Pacific Northwest, Great Basin, and Great Plains regions of the United States. Ventenata was first reported in North America in 1952 in Washington (Old and Callihan 1987) and has since spread to 7 western states in the USA (CA, …

Book Reviews: American Serengeti: The Last Big Animals Of The Great Plains. Dan Flores., Daniel S. Licht

The Prairie Naturalist

Before describing what Flores’ book is, I must state what it is not. It is not a technical book designed for scholarly readers. Sources are not fully cited, and the bibliography is of limited scope. Nor is it a comprehensive book of all the megafauna of the Great Plains. Although chapters are devoted to extant species such as American bison (Bison bison), pronghorn (Antilocapra americana), and coyote (Canis latrans), there are only passing references to mule and white-tailed deer (Odocoileus hemionus and O. virginianus, respectively), elk (Cervus canadensis), and bighorn sheep (Ovis canadensis). Rather, Flores devotes chapters to grizzly bears …

Diel And Monthly Movement Rates By Migratory And Resident Female Pronghorn, Paul F. Jones, T. Andrew Hurly, Chelsea Jensen, Karl Zimmer, Andrew Jakes

The Prairie Naturalist

Animal movement patterns are variable, with certain species primarily being diurnal and others nocturnal. Pronghorn (Antilocapra americana) are regarded as diurnal animals moving predominately during daylight hours. Anecdotal accounts, however, suggest that pronghorn move during the night but the extent, frequency, and importance of these nocturnal movement behaviors are unknown. To evaluate movements, we combined global positioning system relocation data from collared female pronghorn in the Northern Sagebrush Steppe between 2003 and 2007 with sunrise/sunset data within a geographical information system platform. We assessed whether mean and maximum movement rates were influenced by diel period (dawn, day, dusk, and night), …

The Pitfalls Of Data Analysis, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! I hope summer finds you well and enjoying the Great Plains in some way, whether that be starting a new field season, a long-overdue break from the office, or planning your next family vacation. For me, transitioning away from the demands of the Spring 2017 semester to data analyses and preparation of my own manuscripts are particularly exciting (well, as exciting as “office life” can be!). Over the past month, I have initiated a number of grandiose summer objectives, most of which include analysis or in some instances, re-analysis of data to address concerns raised during peer-review. …

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 49 No. 1

The Prairie Naturalist

TABLE OF CONTENTS

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Diel and Monthly Movement Rates by Migratory and Resident Female Pronghorn Paul F. Jones, T. Andrew Hurley, Chelsea Jensen, Karl Zimmer, and Andrew Jakes

13 Pheasant Response to Lead Ingestion Travis J. Runia and Alex J. Solem

NOTES

19 Examining the Potential Competitive Effects of Ventenata dubia on Annual and Perennial Grasses Shawn McKay, Lesley R. Morris, Christopher E. Morris, and Elizabeth A. Leger

23 Adult Red-Headed Woodpecker Interaction with Bullsnake After Arboreal Nest Depradation Brittany J. Yohannes and James L. Howitz

26 Breeding Trumpeter Swans in Northeastern North Dakota Mark …

Hosting Data Packages Via Drat: A Case Study With Hurricane Exposure Data, G Brooke Anderson, Dirk Eddelbuettel

The R Journal

Data-only packages offer a way to provide extended functionality for other R users. However, such packages can be large enough to exceed the package size limit (5 megabytes) for the Comprehensive R Archive Network (CRAN). As an alternative, large data packages can be posted to additional repostiories beyond CRAN itself in a way that allows smaller code packages on CRAN to access and use the data. The drat package facilitates creation and use of such alternative repositories and makes it particularly simple to host them via GitHub. CRAN packages can draw on packages posted to drat repositories through the use …

Imputets: Time Series Missing Value Imputation In R, Steffen Moritz, Thomas Bartz-Beielstein

The R Journal

The imputeTS package specializes on univariate time series imputation. It offers multiple state-of-the-art imputation algorithm implementations along with plotting functions for time series missing data statistics. While imputation in general is a well-known problem and widely covered by R packages, finding packages able to fill missing values in univariate time series is more complicated. The reason for this lies in the fact, that most imputation algorithms rely on inter-attribute correlations, while univariate time series imputation instead needs to employ time dependencies. This paper provides an introduction to the imputeTS package and its provided algorithms and tools. Furthermore, it gives a …

On Some Extensions To Ga Package: Hybrid Optimisation, Parallelisation And Islands Evolution, Luca Scrucca

The R Journal

Genetic algorithms are stochastic iterative algorithms in which a population of individuals evolve by emulating the process of biological evolution and natural selection. The R package GA provides a collection of general purpose functions for optimisation using genetic algorithms. This paper describes some enhancements recently introduced in version 3 of the package. In particular, hybrid GAs have been implemented by including the option to perform local searches during the evolution. This allows to combine the power of genetic algorithms with the speed of a local optimiser. Another major improvement is the provision of facilities for parallel computing. Parallelisation has been …

Dgaselid: An R Package For Selecting A Variable Number Of Features In High Dimensional Data, Nicolae Teodor Melita, Stefan Holban

The R Journal

The dGAselID package proposes an original approach to feature selection in high dimensional data. The method is built upon a diploid genetic algorithm. The genotype to phenotype mapping is modeled after the Incomplete Dominance Inheritance, over passing the necessity to define a dominance scheme. The fitness evaluation is done by user selectable supervised classifiers, from a broad range of options. Cross validation options are also accessible. A new approach to crossover, inspired from the random assortment of chromosomes during meiosis is included. Several mutation operators, inspired from genetics, are also proposed. The package is fully compatible with the data formats …

Descriptions, Notes And Reassignments In Neoibidionini (Coleoptera: Cerambycidae: Cerambycinae) With A New Genus, Three New Species And Keys To Species Of Brechmoidion Martins, 1969, Compsibidion Thomson, 1864 And Rhysium Pascoe, 1866, Antonio Santos-Silva, Maria Helena M. Galileo, James E. Wappes

Insecta Mundi

Chiquitano gen. nov. Chiquitano volcanesensis sp. nov., Compsibidion achiraensis sp. nov. and Compsibidion amboroensis sp. nov. (Coleoptera: Cerambycidae: Cerambycinae: Neoibidionini) are described from Bolivia. Notes on Rhysium Pascoe, 1866 and Rhysium bimaculatum Pascoe, 1866 are provided, and Brechmoidion separatum Martins and Galileo, 2007 is transferred to Rhysium. Keys to species of Compsibidion Thomson, 1864, Brechmoidion Martins, 1969 and Rhysium Pascoe, 1866 are also provided.

Retrieval And Analysis Of Eurostat Open Data With The Eurostat Package, Leo Lahti, Janne Huovari, Markus Kainu, Przemysław Biecek

The R Journal

The increasing availability of open statistical data resources is providing novel opportunities for research and citizen science. Efficient algorithmic tools are needed to realize the full potential of the new information resources. We introduce the eurostat R package that provides a collection of custom tools for the Eurostat open data service, including functions to query, download, manipulate, and visualize these data sets in a smooth, automated and reproducible manner. The online documentation provides detailed examples on the analysis of these spatio-temporal data collections. This work provides substantial improvements over the previously available tools, and has been extensively tested by an …

Isogenegui: Multiple Approaches For Dose-Response Analysis Of Microarray Data Using R, Martin Otava, Rudradev Sengupta, Ziv Shkedy, Dan Lin, Setia Pramana, Tobias Verbeke, Philippe Haldermans, Ludwig A. Hothorn, Daniel Gerhard, Rebecca M. Kuiper, Florian Klinglmueller, Adetayo Kasim

The R Journal

The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives under the assumption of order restriction. We introduce the new R package IsoGene Graphical User Interface (IsoGeneGUI), an extension of the original IsoGene package that includes methods from most of available R packages designed for the analysis of order restricted microarray data, namely orQA, ORIClust, goric and ORCME. The methods included in the new …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. Bioconductor 3.5 was released on 25 April, 2017. It is compatible with R 3.4 and consists of 1383 software packages, 316 experiment data packages, and 911 up-to-date annotation packages. The release announcement includes descriptions of 88 new packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

Timber Talk, Vol. 55, No. 2, June 2017

Timber Talk: Nebraska Forest Industry Newsletter

In This Issue

Lumber Market Reports 1

Hardwood Lumber Prices 2

Letter from the Editor: Nebraska Forest Products Association Can Nebraska’s beef industry be a model for the forest products industry? 3

American Wood Fibers--Yes Virginia, there is pine in Nebraska...And it has value! 4

Pine Ridge Sawmill Ready to Come Back to Life--Doescher Mill looking to rent/lease complete sawmill operation 5

Workshop Announcement--Portable Sawmill Operations and Lumber Drying 6

Nebraska Forest Service Awarded Biochar Grant 6

Nebraska Forest Industry Spotlight 7

Forest Products Specialists Tour Nebraska Facilities 7

Timber Sales 8

Intraguild Interactions And Behavior Of Spodoptera Frugiperda And Helicoverpa, José P. F. Bentivenha, Débora Goulart Montezano, Thomas E. Hunt, Edson L. L. Baldin, Julie A. Peterson, Vinicius S. Victor, Luiz E. R. Pannuti, Ana María Vélez, Silvana L. Vieira De Paula Moraes

Department of Entomology: Faculty Publications

Background: Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), is one of the major pests of maize, and is in the same feeding guild of the noctuid pests, Helicoverpa zea (Boddie), and H. armigera (Hübner), recently reported in South and North America. The intraguild interactions of these species were assessed in laboratory and field conditions by determining the survival of larvae in interactions scenarios with non-Bt maize silks and ears. Moreover, a video-tracking system was utilized to evaluate behavioral parameters during larval interactions in scenarios with or without food.

Results: In intraguild interactions, S. frugiperda had greater survival (55 …

First Report Of Xanthomonas Vasicola Causing Bacterial Leaf Streak On Corn In The United States, K. A. Korus, J. M. Lang, A. O. Adesemoye, C. C. Block, N. Pal, J. E. Leach, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

In 2014 and 2015, Zea mays samples (field, seed, and popcorn) were submitted to the Plant and Pest Diagnostic Clinic at the University of Nebraska–Lincoln displaying long, dark, yellow to brown, water-soaked, linear lesions confined to the interveinal spaces of the leaves. Initial symptoms appeared as small water-soaked flecks that expanded between veins to form irregular lesions. In some cases, the disease progressed to cover 40 to 50% of the leaf area. The disease was confirmed by symptom expression and bacterial streaming in 41 counties in Nebraska as well as Yuma Co., Colorado, and Phillips Co., Kansas, both contiguous to …

Cover Crops: A Primer, Joshua J. Miller, Katja Koehler-Cole, Rodrigo Werle, Daren Redfearn

Department of Plant Pathology: Faculty Publications

When deciding how best to use cover crops, it is important to consider the ultimate goal. Is it to increase soil organic matter, increase nutrient availability to subsequent crops, reduce soil compaction, supply forage for livestock, and/or suppress weeds? Answering these questions will help identify the cover crops that offer the best chance of success for meeting the goal. Primarily, cover crops are used to enhance soil conservation, nutrient cycling and supply, and weed control. However, these benefits vary based on the species of cover crop that is planted, so it is important to select the crop type that will …

Geometry-Based Mass Grading Of Mango Fruits Using Image Processing, M. A. Momin, Md Towfiqur Rahman, M. S. Sultana, C. Igathinathane, A. T. M. Ziauddin, T. E. Grift

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Mango (Mangifera indica) is an important, and popular fruit in Bangladesh. However, the post-harvest processing of it is still mostly performed manually, a situation far from satisfactory, in terms of accuracy and throughput. To automate the grading of mangos (geometry and shape), we developed an image acquisition and processing system to extract projected area, perimeter, and roundness features. In this system, images were acquired using a XGA format color camera of 8-bit gray levels using fluorescent lighting. An image processing algorithm based on region based global thresholding color binarization, combined with median filter and morphological analysis was developed …

Nitrogen Addition And Ecosystem Functioning: Changes In Species Composition Leaf Traits Amplify Increases In Leaf Area Index And Canopy Chlorophyll, Anna R. Tatarko

School of Biological Sciences: Dissertations, Theses, and Student Research

Increased nutrient inputs can cause shifts in plant community composition and plant functional traits, both of which affect ecosystem function. We studied community- and species-level changes in specific leaf area (SLA), chlorophyll, leaf thickness, leaf toughness, plant height and leaf dry matter content (LDMC) in a full factorial nitrogen (N), phosphorus (P), potassium (K) fertilization experiment in a semi-arid grassland. Nitrogen was the only nutrient addition to significantly affect leaf functional traits, and N addition increased community weighted SLA by 19%, leaf chlorophyll content by 34%, height by 26%, and resulted in an 11% decrease in LDMC while leaf thickness …

Adult Red-Headed Woodpecker Interaction With Bullsnake After Arboreal Nest Depredation, Brittney J. Yohannes, James L. Howitz

The Prairie Naturalist

Nest success rates often are higher among cavity-nesting birds than those that nest in open cups or on the ground. Among cavity-nesting birds, woodpeckers have some of the highest rates of nest success. A review of woodpecker nesting ecology across species documented nest success ranging from 0.42 to 1.00 with a median of 0.80 (n = 84 populations), and that predation was low, ranging from 0.00 to 0.35 with a median of 0.13 (n = 33 populations). The constrained opening to a cavity nest limits predation to relatively small animals or those able to break open cavity walls. …

Breeding Trumpeter Swans In Northeast- Ern North Dakota, Mark R. Fisher, Matthew D. Sprenger, Chris R. Roed, David O. Lambeth

The Prairie Naturalist

The trumpeter swan (Cygnus buccinator) is North America’s largest waterfowl species and breeds in wetland habitats across the northern United States, Alaska and Canada. Summer observations by ornithologists, including those of John James Audubon in 1843, indicated a substantial number of trumpeter swans were breeding in North Dakota prior to European settlement. However, the species was extirpated by the late 1800s and there were no subsequent breeding records for over a century (Stewart 1975). Since 2007, 5 recent nesting records indicate that trumpeter swan has returned as a regular breeding species in North Dakota.

A continental range-wide breeding trumpeter swan …

Erratum

The Prairie Naturalist

In the June 2016 issue (48:1, page 56), the Editorial Staff inadvertently omitted corrections provided by the corresponding author prior to publication. In the second paragraph of the left column (i.e., 5 lines from the bottom), “is” should be replaced with “could be.” Similarly, in the right column (9 lines from the top), “In additional” should be replaced with “In addition.” On page 58, the following text should be placed after “institutions” in the Appendix caption: “University of Central Missouri (CMSU), Truman State University (TSU).” Lastly, within the appendix, all instances of MHP should be replaced with FHSM and “OF” …

Using Network Sampling And Recruitment Data To Understand Social Structures Related To Community Health In A Population Of People Who Inject Drugs In Rural Puerto Rico, Mayra Coronado-García, Courtney R. Thrash, Melissa L. Welch-Lazoritz, G. Robin Gauthier, Juan Carlos Reyes, Bilal Khan, Kirk Dombrowski

Department of Sociology: Faculty Publications

Objective: This research examined the social network and recruitment patterns of a sample of people who inject drugs (PWIDs) in rural Puerto Rico, in an attempt to uncover systematic clustering and between-group social boundaries that potentially influence disease spread.

Methods: Respondent driven sampling was utilized to obtain a sample of PWID in rural Puerto Rico. Through eight initial “seeds”, 317 injection drug users were recruited. Using recruitment patterns of this sample, estimates of homophily and affiliation were calculated using RDSAT.

Results: Analyses showed clustering within the social network of PWID in rural Puerto Rico. In particular, females showed a very …

Use Of Satellite Trap Transmitters In Capturing Mountain Lions, Randy D. Johnson, Jonathan A. Jenks, Stephanie A. Tucker

The Prairie Naturalist

The use of safe and humane methods for the capture of wild animals is imperative in wildlife research, wildlife damage management, and feral animal control. When capturing animals successfully and humanely, several items must be addressed, including animal safety, personnel safety, non-target captures, and cost (Sikes et al. 2016). Additionally, public pressures against the use of traps have led to significant changes in trapping regulations across North America and beyond (Andelt et al. 1999, Darrow and Shivik 2008) and can place research projects at risk to loss of Institutional Animal Care and Use Committee (IACUC) approval (Larkin et al. 2003). …

Pgee: An R Package For Analysis Of Longitudinal Data With High-Dimensional Covariates, Gul Inan, Lan Wang

The R Journal

We introduce an R package PGEE that implements the penalized generalized estimating equations (GEE) procedure proposed by Wang et al. (2012) to analyze longitudinal data with a large number of covariates. The PGEE package includes three main functions: CVfit, PGEE, and MGEE. The CVfit function computes the cross-validated tuning parameter for penalized generalized estimating equations. The function PGEE performs simultaneous estimation and variable selection for longitudinal data with high-dimensional covariates; whereas the function MGEE fits unpenalized GEE to the data for comparison. The R package PGEE is illustrated using a yeast cell-cycle gene expression data set.

Mdplot: Visualise Molecular Dynamics, Christian Margreitter, Chris Oostenbrink

The R Journal

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMSD/RMSF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package’s functions, give examples of the function …

Implementing A Metapopulation Bass Diffusion Model Using The R Package Desolve, Jim Duggan

The R Journal

Diffusion is a fundamental process in physical, biological, social and economic settings. Consumer products often go viral, with sales driven by the word of mouth effect, as their adoption spreads through a population. The classic diffusion model used for product adoption is the Bass diffusion model, and this divides a population into two groups of people: potential adopters who are likely to adopt a product, and adopters who have purchased the product, and influence others to adopt. The Bass diffusion model is normally captured in an aggregate form, where no significant consumer differences are modeled. This paper extends the Bass …

Aliner: An R Package For Optimizing Feature-Weighted Alignments And Linguistic Distances, Sean S. Downey, Guowei Sun, Peter Norquest

The R Journal

Linguistic distance measurements are commonly used in anthropology and biology when quantitative and statistical comparisons between words are needed. This is common, for example, when analyzing linguistic and genetic data. Such comparisons can provide insight into historical population patterns and evolutionary processes. However, the most commonly used linguistic distances are derived from edit distances, which do not weight phonetic features that may, for example, represent smaller-scale patterns in linguistic evolution. Thus, computational methods for calculating feature-weighted linguistic distances are needed for linguistic, biological, and evolutionary applications; additionally, the linguistic distances presented here are generic and may have broader applications in …

Minval: An R Package For Minimal Validation Of Stoichiometric Reactions, Daniel Osorio, Janneth González, Andrés Pinzón

The R Journal

A genome-scale metabolic reconstruction is a compilation of all stoichiometric reactions that can describe the entire cellular metabolism of an organism, and they have become an indispensable tool for our understanding of biological phenomena, covering fields that range from systems biology to bioengineering. Interrogation of metabolic reconstructions are generally carried through Flux Balance Analysis, an optimization method in which the biological sense of the optimal solution is highly sensitive to thermodynamic unbalance caused by the presence of stoichiometric reactions whose compounds are not produced or consumed in any other reaction (orphan metabolites) and by mass unbalance. The minval package was …

Network Visualization With Ggplot2, Sam Tyner, François Briatte, Heike Hofmann

The R Journal

This paper explores three different approaches to visualize networks by building on the grammar of graphics framework implemented in the ggplot2 package. The goal of each approach is to provide the user with the ability to apply the flexibility of ggplot2 to the visualization of network data, including through the mapping of network attributes to specific plot aesthetics. By incorporating networks in the ggplot2 framework, these approaches (1) allow users to enhance networks with additional information on edges and nodes, (2) give access to the strengths of ggplot2, such as layers and facets, and (3) convert network data objects …