Digital Commons Network^™

Ggfortify: Unified Interface To Visualize Statistical Results Of Popular R Packages, Yuan Yuan, Masaaki Horikoshi, Wenxuan Li

The R Journal

The ggfortify package provides a unified interface that enables users to use one line of code to visualize statistical results of many R packages using ggplot2 idioms. With the help of ggfortify, statisticians, data scientists, and researchers can avoid the sometimes repetitive work of using the ggplot2 syntax to achieve what they need.

Ake: An R Package For Discrete And Continuous Associated Kernel Estimations, Wanbitching E. Wansouwé, Sobom M. Somé, Célestin C. Kokonendji

The R Journal

Kernel estimation is an important technique in exploratory data analysis. Its utility relies on its ease of interpretation, especially based on graphical means. The Ake package is introduced for univariate density or probability mass function estimation and also for continuous and discrete regression functions using associated kernel estimators. These associated kernels have been proposed due to their specific features of variables of interest. The package focuses on associated kernel methods appropriate for continuous (bounded, positive) or discrete (count, categorical) data often found in applied settings. Furthermore, optimal bandwidths are selected by cross-validation for any associated kernel and by Bayesian methods …

Eicompare: Comparing Ecological Inference Estimates Across Ei And Ei:Rc, Loren Collingwood, Kassra Oskooii, Sergio Garcia-Rios, Matt Barreto

The R Journal

Social scientists and statisticians often use aggregate data to predict individual-level behavior because the latter are not always available. Various statistical techniques have been developed to make inferences from one level (e.g., precinct) to another level (e.g., individual voter) that minimize errors associated with ecological inference. While ecological inference has been shown to be highly problematic in a wide array of scientific fields, many political scientists and analysis employ the techniques when studying voting patterns. Indeed, federal voting rights lawsuits now require such an analysis, yet expert reports are not consistent in which type of ecological inference is used. This …

Calculating Biological Module Enrichment Or Depletion And Visualizing Data On Large-Scale Molecular Maps With Acsnminer And Rnavicell Packages, Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Zinovyev, Eric Bonnet

The R Journal

Biological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, the Atlas of Cancer Signaling Network (ACSN) being an example. All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe ACSNMineR for calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSNmolecular pathways gene sets, but can use any gene set encoded as a GMT file, …

Escape From Boxland, Barret Schloerke, Hadley Wickham, Dianne Cook, Heike Hofmann

The R Journal

A library of common geometric shapes can be used to train our brains for understanding data structure in high-dimensional Euclidean space. This article describes the methods for producing cubes, spheres, simplexes, and tori in multiple dimensions. It also describes new ways to define and generate high-dimensional tori. The algorithms are described, critical code chunks are given, and a large collection of generated data are provided. These are available in the R package geozoo, and selected movies and images, are available on the GeoZoo web site (http://schloerke.github.io/geozoo/)

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

CRAN growth

New CRAN task views

New packages in CRAN task views

Easyroc: An Interactive Web-Tool For Roc Curve Analysis Using R Language Environment, Dincer Goksuluk, Selcuk Korkmaz, Gokmen Zararsiz, A Ergun Karaagaoglu

The R Journal

ROC curve analysis is a fundamental tool for evaluating the performance of a marker in a number of research areas, e.g., biomedicine, bioinformatics, engineering etc., and is frequently used for discriminating cases from controls. There are a number of analysis tools which are used to guide researchers through their analysis. Some of these tools are commercial and provide basic methods for ROC curve analysis while others offer advanced analysis techniques and a command-based user interface, such as the R environment. The R environment includes comprehensive tools for ROC curve analysis; however, using a command-based interface might be challenging and time …

Hdm: High-Dimensional Metrics, Victor Chernozhukov, Chris Hansen, Martin Spindler

The R Journal

In this article the package High-dimensional Metrics hdm is introduced. It is a collection of statistical methods for estimation and quantification of uncertainty in high-dimensional approximately sparse models. It focuses on providing confidence intervals and significance testing for (possibly many) low-dimensional subcomponents of the high-dimensional parameter vector. Efficient estimators and uniformly valid confidence intervals for regression coefficients on target variables (e.g., treatment or policy variable) in a high-dimensional approximately sparse regression model, for average treatment effect (ATE) and average treatment effect for the treated (ATET), as well for extensions of these param eters to the endogenous setting are provided. Theory …

Distance Measures For Time Series In R: The Tsdist Package, Usue Mori, Alexander Mendiburu, Jose A. Lozano

The R Journal

The definition of a distance measure between time series is crucial for many time series data mining tasks, such as clustering and classification. For this reason, a vast portfolio of time series distance measures has been published in the past few years. In this paper, the TSdist package is presented, a complete tool which provides a unified framework to calculate the largest variety of time series dissimilarity measures available in R at the moment, to the best of our knowledge. The package implements some popular distance measures which were not previously available in R, and moreover, it also provides wrappers …

Condsurv: An R Package For The Estimation Of The Conditional Survival Function For Ordered Multivariate Failure Time Data, Luis Meira-Machado, Meira-Machado Sestelo

The R Journal

One major goal in clinical applications of time-to-event data is the estimation of survival with censored data. The usual nonparametric estimator of the survival function is the time-honored Kaplan-Meier product-limit estimator. Though this estimator has been implemented in several R packages, the development of the condSURV R package has been motivated by recent contributions that allow the estimation of the survival function for ordered multivariate failure time data. The condSURV package provides three different approaches all based on the Kaplan-Meier estimator. In one of these approaches these quantities are estimated conditionally on current or past covariate measures. Illustration of the …

Measurement Units In R, Edzer Pebesma, Thomas Mailund, James Hiebert

The R Journal

We briefly review SI units, and discuss R packages that deal with measurement units, their compatibility and conversion. Built upon udunits2 and the UNIDATA udunits library, we introduce the package units that provides a class for maintaining unit metadata. When used in expression, it automatically converts units, and simplifies units of results when possible; in case of incompatible units, errors are raised. The class flexibly allows expansion beyond predefined units. Using units may eliminate a whole class of potential scientific programming mistakes. We discuss the potential and limitations of computing with explicit units.

Tigris: An R Package To Access And Work With Geographic Data From The Us Census Bureau, Kyle Walker

The R Journal

TIGER/Line shapefiles from the United States Census Bureau are commonly used for the mapping and analysis of US demographic trends. The tigris package provides a uniform interface for R users to download and work with these shapefiles. Functions in tigris allow R users to request Census geographic datasets using familiar geographic identifiers and return those datasets as objects of class "Spatial*DataFrame". In turn, tigris ensures consistent and high-quality spatial data for R users’ cartographic and spatial analysis projects that involve US Census data. This article provides an overview of the functionality of the tigris package, and concludes with an applied …

Mixtox: An R Package For Mixture Toxicity Assessment, Xiang-Wei Zhu, Jian-Yi Chen

The R Journal

Mixture toxicity assessment is indeed necessary for humans and ecosystems that are continually exposed to a variety of chemical mixtures. This paper describes an R package, called mixtox, which offers a general framework of curve fitting, mixture experimental design, and mixture toxicity prediction for practitioners in toxicology. The unique features of mixtox include: (1) constructing a uniform table for mixture experimental design; and (2) predicting toxicity of a mixture with multiple components based on reference models such as concentration addition, independent action, and generalized concentration addition. We describe the various functions of the package and provide examples to illustrate their …

Water: Tools And Functions To Estimate Actual Evapotranspiration Using Land Surface Energy Balance Models In R, Guillermo Federico Olmedo, Samuel Ortega-Farías, Daniel De La Fuente-Sáiz, David Fonseca- Luego, Fernando Fuentes-Peñailillo

The R Journal

The crop water requirement is a key factor in the agricultural process. It is usually estimated throughout actual evapotranspiration (ETa). This parameter is the key to develop irrigation strategies, to improve water use efficiency and to understand hydrological, climatic, and ecosystem processes. Currently, it is calculated with classical methods, which are difficult to extrapolate, or with land surface energy balance models (LSEB), such as METRIC and SEBAL, which are based on remote sensing data. This paper describes water, an open implementation of LSEB. The package provides several functions to estimate the parameters of the LSEB equation from satellite data …

Burwell Fall Field Days, Janis Paseka

Nebraska Bird Review

The meeting of2016 NOU Fall Field Days took place at the Burwell Legion Club on Sept. 30–Oct. 2, 2016. There were about 50 in attendance at the meeting, which was organized by Robin Harding, Lanny Randolph, and Betty Grenon.

On Friday evening Chad Christiansen, who works for the U. S. Fish and Wildlife Service at the Fort Niobrara/Valentine National Wildlife Refuge Complex, spoke about the goals of the Natural Legacy Project to identify a set of priority landscapes that, if properly managed, would conserve the majority of Nebraska's biological diversity. These landscapes, called Biologically Unique Landscapes, were selected based on …

Nebraska Bird Review (December 2016) 84(4), Whole Issue

Nebraska Bird Review

Fall Field Report, August–November 2016 ... 154

In Memory of Elizabeth Grenon … 180

Burwell Fall Field Days ... 182

Index to Volume 84 … 187

Subscription and Organization Information ... 203

Development Of Psychometrically Equivalent Speech Recognition Threshold Materials For Native Cebuano Speakers, Melissa Dawn Anderson

Theses and Dissertations

While there is a clear and immediate need for reliable speech audiometry materials to evaluate the speech recognition threshold (SRT), these recorded materials are not available in Cebuano, a language of the Philippines with 15.8 million speakers. The purpose of this study was to develop, digitally record, evaluate, and psychometrically equate a set of Cebuano trisyllabic words for use in measuring the SRT. To create the SRT materials, common Cebuano trisyllabic words were digitally recorded by a male talker of Cebuano and presented for evaluation to 20 native speakers of Cebuano with normal hearing. Based on psychometric performance, a set …

Finnish Teacher Collaboration: The Behaviors, Learning, And Formality Of Teacher Collaboration, Bruce H. Eschler

Theses and Dissertations

Finnish teachers continue to receive significant attention among educators, educational leaders, and policy makers in the United States and around the globe. In addition, teacher collaboration continues to receive support as a meaningful part of teacher work and practice. Teacher collaboration is frequently described in various ways within different contexts. This study aims to: (a) better understand the nature of Finnish teacher collaboration by examining three teacher collaboration behaviors (sharing information and knowledge, planning, and problem-solving); (b) explore the extent to which Finnish teacher collaboration is formal (or school-required) collaboration and informal (or voluntary) collaboration; and (c) investigate …

The Riemann Hypothesis, Danny Allen, Kyle Bonetta-Martin, Elizabeth Codling, Simon Jefferies

The Plymouth Student Scientist

This literature review provides a brief discussion of the Riemann Hypothesis, a conjecture regarding the location of the zeros on the Riemann zeta function. We also look at the implications of solving the hypothesis, and investigate historical attempts to solve the conjecture.

Analysis Of Manufacturing Parameters On The Shear Strength Of Aluminium/Gfrp Co-Cured And Adhesively Bonded Single-Lap Joints, Ashley Reburn

The Plymouth Student Scientist

Due to the increased application of composite materials in recent years, the process of joining composites to metals has become a key area of interest. As a result, methods to increase the strength of composite-to-metal joints are highly sought after. Since the mechanical behaviour of composite-to-metal joints depends on many manufacturing parameters. An experimental and numerical study into the shear strength behaviour of GFRP-to-aluminium single-lap joints was performed to investigate the effect of four manufacturing parameters, with the aim of optimising shear strength. For one manufacturing parameter, a relatively new joining process, co-curing, is studied, and results are benchmarked against …

Distributed Multi-Component Approach And System For Enhanced Security Of Public Infrastructure As A Service (Iaas) Cloud Computing Environments, Jason Nikolai

Masters Theses & Doctoral Dissertations

Cloud computing has become big business with organizations spending millions of dollars creating and deploying cloud solutions. However, adoption of this multi-tenant and dynamic technology has been slowed by security concerns. In this dissertation, to help increase adoption by reducing security risks, we examine three research questions. First, how can we detect attacks on cloud tenant instances without specific knowledge of tenant applications? Second, how can we assist cloud providers with interpretation of the alert output from security controls in an IaaS cloud environment to improve security? And, third, how can we help protect cloud tenants from insider data theft …

How Do Designers Of The Built Environment Attempt To Make Ecological Sustainability Sensory Legible?, Carly L. Bartow

Architecture Undergraduate Honors Theses

This paper attempts to provide a theoretical framework for making ecosystem function and ecologically sustainable design more perceptible or sensible to people through architecture and the built environment. Design features of the Bertschi School Science Wing and the Bullitt Center in Seattle, Washington are incorporated to illustrate the sensory legibility of ecological sustainability criteria.The criteria are available to designers to help educate a building's occupants on environmentally sustainable design and motivate more sustainable behavior.

Acquisition Of Picture Exchange-Based Vs. Signed Mands And Implications To Teach Functional Communication Skills To Children With Autism, Sang S. Nam Ph.D, Young S. Hwang Ph.D

The Journal of Special Education Apprenticeship

A literature review was conducted to describes important concepts involved in functional analysis of verbal behavior as well as to evaluates empirical research findings on acquisition of picture exchange-based vs. signed mands to suggest instructional implications for teachers and therapists to teach functional communication skills to children with autism. Research findings indicate that children with autism acquire picture exchange responses to mand for reinforcing items more easily and rapidly than signed responses. There is also a strong relation between motor imitation, matching skills and sign language acquisition. It is suggested that both motor imitation and matching skills be examined to …

Effects Of Digital-Based Math Fluency Interventions On Learners With Math Difficulties: A Review Of The Literature, Lauren E. Cozad, Paul J. Riccomini

The Journal of Special Education Apprenticeship

Mathematical proficiency serves as a foundation for student success in the classroom and real world. One component of mathematical proficiency is fluency with basic facts. Frequently, students with mathematics difficulties struggle to become proficient and fluent in the four basic operations. Interventions are available to help develop and promote fluency for students. Digital-based interventions, such as programs on computers or tablet applications, are one avenue by which students are able to acquire and maintain fluency. These digital tools are becoming increasingly more common and available in today’s classroom. Eight studies on digital-based fact fluency were identified through a systematic search …

Our Students’ Minds Matter: Integrating Mindfulness Practices Into Special Education Classrooms, Danielle Magaldi Ph.D., Jennie Park-Taylor Ph.D.

The Journal of Special Education Apprenticeship

This article explores the usefulness of mindfulness practices in special education classrooms. Mindfulness is defined as the ability to regulate and control one’s attention with an orientation toward the present moment. Mindfulness practices of breathing, imagery, movement, reflection, and acceptance exercises are described along with research on the social, behavioral, and attentional effects following mindfulness interventions. The article concludes with practical considerations for special educators considering implementing mindfulness practices into curriculum, along with future directions for mindfulness in the field of special education.

Effects Of Tli- Versus Nwea-Interim Assessment On Academic Achievement Of Sixth- And Seventh-Grade Students, Walt Davis

College of Education Dissertations

This project focused on two online providers, The Learning Institute (TLI) and Northwest Evaluation Association (NWEA). The purpose of this dissertation was to provide additional research concerning the effects of interim assessments (TLI versus NWEA) and gender on literacy and mathematics achievement for students in Grades 6 and 7 in Northwest Arkansas. Of the four included school districts, two used TLI and two used NWEA as their interim assessment. For all four hypotheses, the independent variables were gender and interim assessment type. In the first and second hypotheses, the dependent variable was literacy achievement as measured by student performance on …

Campus Climate Task Force, Short-Term Suggestions, Campus Climate Task Force

Campus Climate Assessment

First report from the Campus Climate Task Force Steering Committee, with short-term suggestions.

Spatial Pattern Of Genetic Diversity And Selection In The Mhc Class Ii Drb Of Three Neotropical Bat Species, Arielle Salmier, Benoit De Thoisy, Brigitte Crouau-Roy, Vincent Lacoste, Anne Lavergne

KIP Articles

No abstract provided.

Bulletin Cam, Issue 4, 2016, Faculty Of Engineering University Of Malaya

Archival Material (2010s)

No abstract provided.

Buletin Diet = Bulletin Diet, December, 2016, Faculty Of Medicine University Of Malaya

Archival Material (2010s)

No abstract provided.