Physical Sciences and Mathematics Commons^™

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, …

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 …

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.

Reduced Snow Cover Alters Root-Microbe Interactions And Decreases Nitrification Rates In A Northern Hardwood Forest, Patrick O. Sorensen, Pamela H. Templer, Lynn M. Christenson, Jorge Durán, Timothy J. Fahey, Melany C. Fisk, Peter M. Groffman, Jennifer L. Morse, Adrien C. Finzi

Environmental Science and Management Faculty Publications and Presentations

Snow cover is projected to decline during the next century in many ecosystems that currently experience a seasonal snowpack. Because snow insulates soils from frigid winter air temperatures, soils are expected to become colder and experience more winter soil freeze-thaw cycles as snow cover continues to decline. Tree roots are adversely affected by snowpack reduction, but whether loss of snow will affect root-microbe interactions remains largely unknown. The objective of this study was to distinguish and attribute direct (e.g., winter snow-and/ or soil frost-mediated) vs. indirect (e.g., root-mediated) effects of winter climate change on microbial biomass, the potential activity of …

Regional Mapping Of Flow And Wall Characteristics Of Intracranial Aneurysms, Juan R. Cebral, Xinjie Duan, Piyusha S. Gade, Bong Jae Chung, Fernando Mut, Khaled Aziz, Anne M. Robertson

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

The evolution of intracranial aneurysms (IAs) is thought to be driven by progressive wall degradation in response to abnormal hemodynamics. Previous studies focused on the relationship between global hemodynamics and wall properties. However, hemodynamics, wall structure and mechanical properties of cerebral aneurysms can be non-uniform across the aneurysm wall. Therefore, the aim of this work is to introduce a methodology for mapping local hemodynamics to local wall structure in resected aneurysm specimens. This methodology combines image-based computational fluid dynamics, tissue resection, micro-CT imaging of resected specimens mounted on 3D-printed aneurysm models, alignment to 3D vascular models, multi-photon microscopy of the …

Diet And Foraging Behaviors Of Timber Rattlesnakes, Crotalus Horridus, In Eastern Virginia, Scott M. Goetz, Christopher E. Petersen, Robert K. Rose, John D. Kleopfer, Alan H. Savitzky

Biology Faculty Publications

During a 17-yr telemetry study, we examined the diet and ambush behavior of a population of Crotalus horridus in southeastern Virginia. Forty dietary items were identified from 37 fecal samples. We documented 722 instances of snakes in an ambush posture, 61% of which were in a vertical-tree posture, as if hunting arboreal prey at the base of a tree. The most common prey items were Eastern Gray Squirrels (Sciurus carolinensis), which accounted for 45% of all dietary items and represented an estimated 78% of total biomass consumed by C. horridus. Prey was not consumed in proportion to availability, based on …

Web Aplikacionet Dinamike Me Java Ee, Jetë Leci

Theses and Dissertations

Qëllimi i kësaj teze të shkallës bachelor është bërë për analizimi dhe studimin e platformës më të mirë për zhvillimin e web aplikacioneve dinamike, ky studim nuk paraqet bazat e programimit në Java apo zhvillimin e pjesës së bazës së shënimeve ky studim ofron një pasqyrë të teknologjive dhe framework-ëve për implementimin e aplikacioneve me platformën Java Enterprise Edition. Ky kapitull perfshinë një përmbledhje të shkurtë të studimit dhe përvojës sime së bashku, duke shfaqur një pasqyrë të zhvillimit të aplikacioneve dinamike në web me anë të shpjegimit të secilës pjesë përbërëse të platformës shumë të njohur për realizimin e …

Analizimi Dhe Zhvillimi I Modulit Të Orarit Në Wordpress, Gëzim Rexhepi

Theses and Dissertations

Përdorimi i një orari do të ishte një lehtësim i madh në menaxhimin e ngjarjeve të cilat ndodhin në një festival, si rezultat i kërkesave dhe nevojave për një orar i cili do të ishte lehtë i menaxhueshëm nga festivalet e ndryshme vendosa të zhvilloj ketë orar. Ky orar është dizajnuar dhe implementuar për festivalin “Dokufest”. Mirëpo ky orar mund të përdoret edhe nga festivale të tjera. Ky orar do ju ndihmoj festivaleve të ndryshme që të kenë më të lehtë shtimin e ngjarjeve të ndryshme e pastaj ato ngjarje ti shfaqin në këtë orar i cili është mjaft i …

Siguria Në Php, Shpat Ajvazi

Theses and Dissertations

Që të rezultojë me sukses një softuer duhet të përmbush shumë kritere, disa nga këto kriteret janë: efikasiteti, siguria dhe fleksibiliteti. Pavarësisht rëndësisë së softuerit çdo softuer duhet te ketë sigurinë në nivel të lartë duke mos lejuar të dhënat të përfundojnë në duar të personave të pa autorizuar. Pothuajse çdo ditë krijohen mundësi të reja për të sulmuar softuer-ët që funksionojnë përmes internet kjo tregon se siguria duhet të analizohet dhe që zhvilluesit gjithmonë duhet të ndjekin teknologjinë e fundit. Në pjesën kryesore shqyrtohen problemet dhe sulmet që bëhen në PHP sa i përket aspektit të sigurisë. Siguria e …

Zbatimi I Mpls Vpn Dhe Siguria, Fëllënza Bunjaku

Theses and Dissertations

Viteve të fundit, temat e nivelit bachelor po ballafaqohen me një nga trendet më të mëdha në botën e rrjetave kompjuterike duke zgjuar poashtu edhe interesimin tim për të studiuar dhe punuar këtë temë aktuale por duke marr në shqyrtim zbatimin e Multiprotocol Label Switching-Virtual Private Network dhe Siguria të cilës në vazhdim të këtij punimi do t’i referohemi si (MPLS VPN).

Objektivi kryesor i këtij punimi është të kuptuarit e teknologjisë MPLS VPN përmes përkufizimit të kësaj teknologjie, si dhe paraqitjes së një skenario ku shqyrtohen protokolle të ndryshme të komunikimit. Shumica e ofruesve të shërbimeve (angl. ISP) që …

Analysis Of Groundwater Contaminants Using Aris Dispersion Model, Nirmala P. Ratchagar, S. Senthamilselvi

Applications and Applied Mathematics: An International Journal (AAM)

The paper presents the study of dispersion of contaminants in unsteady laminar flow of an incompressible fluid (groundwater) bounded by an upper porous layer and lower impermeable layer with interphase mass transfer. An analytical solution of unsteady advection dispersion based on Aris-Barton method of moments is presented up to the second moment about the mean in axial direction.

Dielectric Analysis Of Aqueous Poly(L-Glutamic Acid) And Poly-L-(Glutamic Acid4, Tyrosine1) Solutions At High Frequencies From Capacitance Measurements, Jorge Monreal, Tatiana Eggers, Manh-Huong Phan

Physics Faculty Publications

A new parallel-plate capacitor fixture has been designed and successfully used to measure dielectric loss of polyelectrolyte solutions with volumes as low as droplets of 13–26 μL. It is particularly useful when studying polypeptides that are either high-cost or can be synthesized only in limited quantities. The ease with which the fixture can be used to obtain preliminary dielectric loss data yields savings in time and cost. In this study capacitance measurements were performed in a wide range of frequencies between 1 and 800 MHz using an Agilent 4191RF Impedance Analyzer. Accuracy of measurements was carefully examined through a comparison …

Umphlett Qci Dec 2016, Natalie A. Umphlett

High Plains Regional Climate Center: Staff Publications

Highlights for the Basin

Temperature and Precipitation Anomalies

Drought Conditions

Large Fires Impact Region

Heavy Rains Bring Flooding to Montana

Isolated Impacts to Agriculture

3-Month Precipitation and Temperature Outlooks

Soil Moisture Conditions

Android Drone: Remote Quadcopter Control With A Phone, Aubrey John Russell

Computer Engineering

The purpose of the “Android Drone” project was to create a quadcopter that can be controlled by user input sent over the phone’s Wi-Fi connection or 4G internet connection. Furthermore, the purpose was also to be able to receive live video feedback over the internet connection, thus making the drone an inexpensive option compared to other, equivalent drones that might cost thousands of dollars. Not only that, but the Android phone also has a host of other useful features that could be utilized by the drone: this includes GPS, pathing, picture taking, data storage, networking and TCP/IP, a Java software …

Impact Of Spatial Averaging On Radar Reflectivity At Internal Snowpack Layer Boundaries, N. Rutter, H.P. Marshall, K. Tape, R. Essery, J. King

CGISS Publications and Presentations

Microwave radar amplitude within a snowpack can be strongly influenced by spatial variability of internal layer boundaries. We quantify the impact of spatial averaging of snow stratigraphy and physical snowpack properties on surface scattering from near-nadir frequency-modulated continuous- wave radar at 12–18 GHz. Relative permittivity, density, grain size and stratigraphic boundaries were measured in-situ at high resolution along the length of a 9 m snow trench. An optimal range of horizontal averaging (4–6 m) was identified to attribute variations in surface scattering at layer boundaries to dielectric contrasts estimated from centimetre-scale measurements of snowpack stratigraphy and bulk layer properties. Single …

In-Column Polymer Modifications: Advancing Polymer Bonded Phases, Alexis G. Huckabee

Open Access Dissertations

Glycosylation is the most common post-translational modification affecting protein activities, including delivery to cell surface, binding affinity, and mediating different physiological effects. Separations of glycoproteins and their glycoforms are essential for drug discovery and development, identification of potential disease biomarkers and quality control. The efficiency of glycoprotein separations is limited by the bonded phases, requiring advances in chromatographic materials. Such advances would improve resolution, allowing for more species to be isolated from a mixture and studied.

Our group found that submicrometer nonporous silica stationary phases with tethered polymer chains (acrylamide) give excellent hydrophilic liquid chromatography (HILIC), a common method used …

Group Transformation And Identification With Kernel Methods And Big Data Mixed Logistic Regression, Chao Pan

Open Access Dissertations

Exploratory Data Analysis (EDA) is a crucial step in the life cycle of data analysis. Exploring data with effective methods would reveal main characteristics of data and provides guidance for model building. The goal of this thesis is to develop effective and efficient methods for data exploration in the regression setting.

First, we propose to use optimal group transformations as a general approach for exploring the relationship between predictor variables X and the response Y. This approach can be considered an automatic procedure to identify the best characteristic of P( Y|X) under which the relationship …

The Effects Of Anthropogenic Stressors On Mercury Concentrations And Community Composition Of Freshwater Zooplankton, Meredith Powers Jordan

Dissertations and Theses

Methylmercury (MeHg) bioaccumulation in freshwater aquatic systems is impacted by anthropogenic stressors, including climate change and excess nutrients. The goal of this study was to determine how warmer water temperatures and excess nutrients would impact zooplankton communities and phytoplankton concentrations, and in turn increase or decrease MeHg concentrations in freshwater zooplankton. I used a 2x2 factorial design to determine if the interaction of temperature and nutrients would impact plankton metrics and zooplankton MeHg concentrations. Mesocosms were filled with Hg-contaminated water and plankton from Cottage Grove Reservoir, Oregon, a waterbody that has experienced decades of elevated MeHg concentrations and corresponding fish …

Sedimentologic Changes In The Deposits Of An Evolving Lahar-Flood In 2006, Hood River Basin, Mount Hood, Oregon, Matthew Ray Poole

Dissertations and Theses

Over a span of six days from November 2-7, 2006 approximately 43 cm of precipitation fell over the Hood River Basin in Oregon. A lahar was initiated on the Eliot Branch of the Middle Fork Hood River by two or more landslides that occurred on the lateral moraines of the Eliot Glacier on the early part of November 7th, 2006. The Eliot Branch lahar was embedded within the larger regional flood that was occurring in the Hood River Basin and traveled a total of 48 km from the initiation points on the north flank of Mount Hood to the Hood …