Physical Sciences and Mathematics Commons^™

Remembering Paul B. Kannowski, Robert Seabloom

The Prairie Naturalist

I am saddened to report that Dr. Paul Kannowski passed away 3 September 2015, succumbing to cancer. He was 88. A native of Grand Forks, Paul attended the University of North Dakota for his B.S. and M.S. degrees, and the University of Michigan for his Ph.D. He joined the University of North Dakota Biology Department in 1957, retiring in 1990 after 33 years of service

Paul chaired UND’s Biology Department twice, totaling 13 years, considered to be a remarkable achievement by many of us who have been exposed to that task! His leadership was instrumental in the nearly exponential growth …

Variability In The Selection Patterns Of Pronghorn: Are They Really Native Prairie Obligates?, Paul F. Jones, Mike Grue, Mike Suitor, Darren J. Bender, Cormack Gates, Dale Eslinger, Julie Landry-Deboer

The Prairie Naturalist

In Canada, pronghorn (Antilocapra americana) are primarily considered a native prairie obligate because of their reliance on open grassland vegetation communities, although an assessment of local ecological knowledge suggests that pronghorn in Alberta select a variety of habitat from native prairie to cultivated lands. The primary objective of our study was to assess whether pronghorn in Alberta and Saskatchewan are native prairie obligates. Specifically, we addressed the following questions: 1) do individual pronghorn show similar selection patterns for native prairie and, therefore, support the notion that they are prairie obligates; 2) do pronghorn show consistent resource selection patterns …

Remembering The Days Of Old: Data Exploration And Simple Statistics, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! By the time you read this editorial, most of you will probably be enjoying spectacular seasonal changes in the outdoors this autumn and a hint of winter in the air (for those of us in the northern Great Plains region). I write this editorial during my favorite time of year, deer hunting in the Midwest. Temperatures are finally start- ing to resemble the fall and the Christmas Holiday season is just around the corner. Much like my children have images of Santa dancing in their heads on Christmas Eve, each fall I replay images of a trophy …

Notes: Woodpecker Forage Availability In Habi- Tat Disturbances Of The Black Hills, Brian E. Dickerson, Angie K. Ambourn, Mark A. Rumble, Kurt K. Allen, Chad P. Lehman

The Prairie Naturalist

Habitat disturbance events are critical to ecological systems in which some bird species have become specialized. The vegetation community, reduced competition, ability to avoid predators, nest-site characteristics, and forage opportunities within a disturbed ecosystem are all aspects that make it desirable for selection by particular species (Svärdson 1949, Cody 1981, Martin 1998). Specifically, avian species rely on the forest conditions created by fire, insects, and disease (Brawn et al. 2001, Hunter et al. 2001, Devictor et al. 2008). In the Black Hills National Forest (BHNF) of South Dakota,two major types of natural disturbances include wildfires and mountain pine beetle (Dendroctonus …

Estimating Herbaceous Biomass Of Grassland Vegetation Using The Reference Unit Method, Eric D. Boyda, Jack L. Bulter, Lan Xu

The Prairie Naturalist

Aboveground net primary production provides valuable information on wildlife habitat, fire fuel loads, and forage availability. Aboveground net primary production in herbaceous plant communities is typically measured by clipping aboveground biomass. However, the high costs associated with physically harvesting plant biomass may prevent collecting sufficient data to account for natural spatial and temporal variability of vegetation at a landscape scale. Various double-sampling techniques have been developed to increase sample size while reducing cost. We applied a biomass estimation technique previously developed for estimating shrub biomass using representative samples or “reference units” to estimate herbaceous grassland biomass. Our reference units consisted …

Conference Report: User! 2015, Torben Tvedebrink

The R Journal

The11thinternational R user conference, useR! 2015, took place in Aalborg, Denmark, 1–3 July 2015. The Department of Mathematical Sciences, Aalborg University, hosted the conference, which took place in Aalborg Congress and Culture Centre.

Mmpp: A Package For Calculating Similarity And Distance Metrics For Simple And Marked Temporal Point Processes, Hideitsu Hino, Ken Takano, Noboru Murata

The R Journal

A simple temporal point process (SPP) is an important class of time series, where the sample realization of the process is solely composed of the times at which events occur. Particular examples of point process data are neuronal spike patterns or spike trains, and a large number of distance and similarity metrics for those data have been proposed. A marked point process (MPP) is an extension of a simple temporal point process, in which a certain vector valued mark is associated with each of the temporal points in the SPP. Analyses of MPPs are of practical importance because instances of …

Abctools: An R Package For Tuning Approximate Bayesian Computation Analyses, Matthew A. Nunes, Dennis Prangle

The R Journal

Approximate Bayesian computation (ABC) is a popular family of algorithms which perform approximate parameter inference when numerical evaluation of the likelihood function is not possible but data can be simulated from the model. They return a sample of parameter values which produce simulations close to the observed dataset. A standard approach is to reduce the simulated and observed datasets to vectors of summary statistics and accept when the difference between these is below a specified threshold. ABC can also be adapted to perform model choice.

In this article, we present a new software package for R, abctools which provides methods …

Practools: Computations For Design Of Finite Population Samples, Richard Valliant, Jill A. Dever, Frauke Kreuter

The R Journal

PracTools is an R package with functions that compute sample sizes for various types of finite population sampling designs when totals or means are estimated. One-, two-, and three-stage designs are covered as well as allocations for stratified sampling and probability proportional to size sampling. Sample allocations can be computed that minimize the variance of an estimator subject to a budget constraint or that minimize cost subject to a precision constraint. The package also contains some specialized functions for estimating variance components and design effects. Several finite populations are included that are useful for classroom instruction.

Clustvarlv: An R Package For The Clustering Of Variables Around Latent Variables, Evelyne Vigneau, Mingkun Chen, El Mostafa Qannari

The R Journal

The clustering of variables is a strategy for deciphering the underlying structure of a data set. Adopting an exploratory data analysis point of view, the Clustering of Variables around Latent Variables (CLV) approach has been proposed by Vigneau and Qannari (2003). Based on a family of optimization criteria, the CLV approach is adaptable to many situations. In particular, constraints may be introduced in order to take account of additional information about the observations and/or the variables. In this paper, the CLV method is depicted and the R package ClustVarLV including a set of functions developed so far within this framework …

Srcs: Statistical Ranking Color Scheme For Visualizing Parameterized Multiple Pairwise Comparisons With R, Pablo J. Villacorta, José A. Sáez

The R Journal

The problem of comparing a new solution method against existing ones to find statistically significant differences arises very often in sciences and engineering. When the problem instance being solved is defined by several parameters, assessing a number of methods with respect to many problem configurations simultaneously becomes a hard task. Some visualization technique is required for presenting a large number of statistical significance results in an easily interpretable way. Here we review an existing color-based approach called Statistical Ranking Color Scheme (SRCS) for displaying the results of multiple pairwise statistical comparisons between several methods assessed separately on a number of …

Zoib: An R Package For Bayesian Inference For Beta Regression And Zero/One Inflated Beta Regression, Fang Liu, Yunchuan Kong

The R Journal

The beta distribution is a versatile function that accommodates a broad range of probability distribution shapes. Beta regression based on the beta distribution can be used to model a response variable y that takes values in open unit interval (0,1). Zero/one inflated beta (ZOIB) regression models can be applied when y takes values from closed unit interval [0,1]. The ZOIB model is based a piecewise distribution that accounts for the probability mass at 0 and 1, in addition to the probability density within (0,1). This paper introduces an R package– zoib that provides Bayesian inferences for a class of ZOIB …

Vsurf: An R Package For Variable Selection Using Random Forests, Robin Genuer, Jean-Michel Poggi, Christine Tuleau-Malot

The R Journal

This paper describes the R package VSURF. Based on random forests, and for both regression and classification problems, it returns two subsets of variables. The first is a subset of important variables including some redundancy which can be relevant for interpretation, and the second one is a smaller subset corresponding to a model trying to avoid redundancy focusing more closely on the prediction objective. The two-stage strategy is based on a preliminary ranking of the explanatory variables using the random forests permutation-based score of importance and proceeds using a stepwise forward strategy for variable introduction. The two proposals can …

Generalized Hermite Distribution Modelling With The R Package Hermite, David Moriña, Manuel Higueras, Pedro Puig, María Oliveira

The R Journal

The Generalized Hermite distribution (and the Hermite distribution as a particular case) is often used for fitting count data in the presence of over-dispersion or multimodality. Despite this, to our knowledge, no standard software packages have implemented specific functions to compute basic probabilities and make simple statistical inference based on these distributions. We present here a set of computational tools that allows the user to face these difficulties by modelling with the Generalized Hermite distribution using the R package hermite. The package can also be used to generate random deviates from a Generalized Hermite distribution and to use basic …

Numerical Evaluation Of The Gauss Hypergeometric Function With The Hypergeo Package, Robin K. S. Hankin

The R Journal

This paper introduces the hypergeo package of R routines for numerical calculation of hypergeometric functions. The package is focussed on efficient and accurate evaluation of the Gauss hypergeometric function over the whole of the complex plane within the constraints of fixed-precision arithmetic. The hypergeometric series is convergent only within the unit circle, so analytic continuation must be used to define the function outside the unit circle. This short document outlines the numerical and conceptual methods used in the package; and justifies the package philosophy, which is to maintain transparent and verifiable links between the software and Abramowitz and Stegun (1965). …

Treeclust: An R Package For Tree-Based Clustering Dissimilarities, Samuel E. Buttrey, Lyn R. Whitaker

The R Journal

This paper describes treeClust, an R package that produces dissimilarities useful for clustering. These dissimilarities arise from a set of classification or regression trees, one with each variable in the data acting in turn as a the response, and all others as predictors. This use of trees produces dissimilarities that are insensitive to scaling, benefit from automatic variable selection, and appear to perform well. The software allows a number of options to be set, affecting the set of objects returned in the call; the user can also specify a clustering algorithm and, optionally, return only the clustering vector. The …

Editorial, Bettina Grün

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 7, Issue 2 of the R Journal. This issue contains 20 contributed research articles and several contributions to the News and Notes section.

Code Profiling In R: A Review Of Existing Methods And An Introduction To Package Guiprofiler, Angel Rubio, Fernando De Villar

The R Journal

Code analysis tools are crucial to understand program behavior. Profile tools use the results of time measurements in the execution of a program to gain this understanding and thus help in the optimization of the code. In this paper, we review the different available packages to profile R code and show the advantages and disadvantages of each of them. In additon, we present GUIProfiler, a package that fulfills some unmet needs

Package GUIProfiler generates an HTML report with the timing for each code line and the relationships between different functions. This package mimics the behavior of the MATLAB profiler. …

Quantifquantile: An R Package For Performing Quantile Regression Through Optimal Quantization, Isabelle Charlier, Davy Paindaveine, Jérôme Saracco

The R Journal

In quantile regression, various quantiles of a response variable Y are modelled as functions of covariates (rather than its mean). An important application is the construction of reference curves/surfaces and conditional prediction intervals for Y. Recently, a nonparametric quantile regression method based on the concept of optimal quantization was proposed. This method competes very well with k-nearest neighbor, kernel, and spline methods. In this paper, we describe an R package, called QuantifQuantile, that allows to perform quantization-based quantile regression. We describe the various functions of the package and provide examples.

Changes In R, The R Core Team

The R Journal

CHANGES IN R 3.2.3

CHANGES IN R 3.2.2

The R Consortium And The R Foundation, Martyn Plummer

The R Journal

The R Consortium was announced at the useR! 2015 conference in Aalborg, Denmark on 30 June. It is a non-profit organization set up to provide infrastructure for the R community. The purpose of this article is to explain some of the background to the setting up of the Consortium and how it interacts with the R Foundation.

Hemodynamic Analysis Of Fast And Slow Aneurysm Occlusions By Flow Diversion In Rabbits, Bong Jae Chung, Fernando Mut, Ramanathan Kadirvel, Ravi Lingineni, David F. Kallmes, Juan R. Cebral

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

Purpose: To assess hemodynamic differences between aneurysms that occlude rapidly and those occluding in delayed fashion after flow diversion in rabbits. Methods: Thirty-six elastase-induced aneurysms in rabbits were treated with flow diverting devices. Aneurysm occlusion was assessed angiographically immediately before they were sacrificed at 1 (n=6), 2 (n=4), 4 (n=8) or 8 weeks (n=18) after treatment. The aneurysms were classified into a fast occlusion group if they were completely or near completely occluded at 4 weeks or earlier and a slow occlusion group if they remained incompletely occluded at 8 weeks. The immediate post-treatment flow conditions in aneurysms of each …

The Search For Exomoon Radio Emissions, Joaquin P. Noyola

Physics Theses - Archive

The field of exoplanet detection has seen many new developments since the discovery of the first exoplanet. Observational surveys by the NASA Kepler Mission and several other instrument have led to the confirmation of over 1900 exoplanets, and several thousands of exoplanet potential candidates. All this progress, however, has yet to provide the first confirmed exomoon. Since all previous attempts to discover exomoons have failed, a novel method to detect them is proposed in this dissertation, which describes development of the method and its applications to select the best exomoon candidates for observational searches. The main goal of these searches …

Theoretical Prediction Of Materials For Efficient Conversion Of Solar Energy, Pranab Sarker

Physics Dissertations - Archive

Our present work represents a systematic theoretical and computational research to find an affordable material for solar energy application using density functional theory (DFT) and post-DFT such as DFT+U and DFT-HSE06. Here, we predict a new photovoltaic material (CuSnW2O8) and a new photocatalyst (ZnSnW2O8). In addition, a new method for predicting the higher power conversion efficiency (PCE) optimized growth conditions will be presented. It is well known that all physical properties are calculated once crystal structure is known. However, knowing crystal structure is extremely challenging and to date, there is no success has been claimed in the case of a …

Structure-Activity Relationships Of Ruthenium(Ii) Polypyridyl Complexes With Redox-Active Intercalating Ligands: Correlation Between Redox Activity, Dna Cleavage Capability And Cytotoxicity, Eugenia Soyo Narh

Chemistry & Biochemistry Theses - Archive

The investigation and development of transition metal complexes as cancer chemotherapeutics has gained a lot of interest in the past few decades and has become a promising area of research. Metal complexes of platinum and ruthenium in particular that have demonstrated success as anticancer drugs or are under exploration currently for clinical use are highlighted in Chapter 1. Chapter 2 describes studies undertaken to understand the neurotoxicity of ruthenium(II) polypyridyl complexes (RPCs), including toxicity in mice and inhibition of the enzyme acetylcholinesterase (AChE), as previous work by Dwyer demonstrated that RPCs could be acutely toxic in mice, presumably due to …

Synthesis Of Modified Ribose Spin-Label, Ke-Wei Chang

Chemistry & Biochemistry Theses - Archive

Transfer ribonucleic acids (tRNAs) from all organisms contain modified nucleosides, which are derived from four different nucleosides. Research has indicated that tRNA modifications affect translation and various metabolic pathways. Among these modifications, some of them need more than one enzyme to produce specific nucleosides. Researchers are interested in investigating the fundamental mechanisms and function of post-transcriptional modifying enzymes. A number of these enzymes are metal-dependent, such as MiaB and MiaE. MiaE enzyme (2-methylthio-N6-isopentenyl-adenosine(37)-tRNA monooxygenase) stereospecifically hydroxylates an adeonosine derivative at the 37th position of tRNA, ms2i6A37, to complete the hypermodification of 2-methylthio-N6-(4-hydroxyisopentenyl)-adenosine (ms2io6A37). Several studies showed that the ms2io6A37 modification …

Siguria E Rrjetave Kompjuterike, Blinera Ahmeti

Theses and Dissertations

Shpërndarja e internetit në përmasa më të mëdha filloi në fillim të viteve 1980. Qysh në këtë fillim lindi edhe nevoja për sigurinë e rrjetave kompjuterike, menjëherë pas shfaqjes së sulmeve të para që shkaktuan dëme në informacionet dhe sistemet kompjuterike. Ndryshimet shumë të shpejta në botën e kompjuterikës, aplikacioneve mobile dhe rrjetave pa kabllo kanë ndryshuar plotësisht tiparet e sigurisë së rrjetave. Qysh nga ajo kohë, sado që ka pasur zhvillime tepër të mëdha në botën e internetit, ende ka shumë ngecje në zhvillimin e metodave të sigurisë së rrjetave.

Problemet me sigurinë më së lehti dhe më së …

Programimi Paralel Me Gpu, Kujtim Kërqeli

Theses and Dissertations

No abstract provided.

Implementimi Dhe Adaptimi I E-Commerce Në Kompanitë E Vogla Në Zvicër, Drilon Tahiri

Theses and Dissertations

Qëllimi i këtij hulumtimi është të shqyrtojë implementimin dhe adaptimin e e-commerce në kompanitë e vogla në Zvicër . Ky hulumtim përshkruan të gjitha përfitimet dhe pengesat me të cilat ballafaqohen kompanitë e vogla gjatë procesit të implementimit të e-commerce. Një hulumtim cilësor është kryer. Po ashtu është kryer edhe një intervistë me një menaxher të një kompanie të vogël në Zvicër.

Ky studim tregon se kompanitë e vogla në Zvicër kanë përparësi në implementimin dhe adaptimin e e-commerce në krahasim me vendet e tjera të Evropës, por ende ka pengesa të cilat mund të përmirësohen në të ardhmen.

Përfitimet …

Krahasimi I Teknologjive Për Implementimin Dhe Përkrahjen E Videove Në Ueb, Rinor Svarça

Theses and Dissertations

Në këtë punim diplome jemi munduar të analizojmë dy teknologjitë më të përdorura për lansimin e videove në internet Adobe Flash dhe HTML5, edhe pse nuk janë të ngjashme kanë të përbashkët mundësinë e shfaqjes së videove në ueb faqe, ku dhe jemi fokusuar më shumë në këtë të përbashkët të këtyre dy teknologjive. Gjithashtu kemi hulumtuar për historikun, zhvillimin, ngjashmëritë dhe dallimet që kanë, kemi analizuar edhe problemet e tye dhe si ka ardhur deri te zëvendësimi i Flash me HTML5 për një kohë mjaftë të shkurtër. Jemi munduar t’i krahasojmë të gjitha pjesët e përbashkëta dhe kemi paraqitur …