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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 …

Bsgs: Bayesian Sparse Group Selection, Kuo-Jung Lee, Ray-Bing Chen

The R Journal

An R package BSGS is provided for the integration of Bayesian variable and sparse group selection separately proposed by Chen et al. (2011) and Chen et al. (in press) for variable selection problems, even in the cases of large p and small n. This package is designed for variable selection problems including the identification of the important groups of variables and the active variables within the important groups. This article introduces the functions in the BSGS package that can be used to perform sparse group selection as well as variable selection through simulation studies and real data.

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 …

Fitting Conditional And Simultaneous Autoregressive Spatial Models In Hglm, Moudud Alam, Lars Rönnegård, Xia Shen

The R Journal

We present a new version ( 2.0) of the hglm package for fitting hierarchical generalized linear models (HGLMs) with spatially correlated random effects. CAR() and SAR() families for con ditional and simultaneous autoregressive random effects were implemented. Eigen decomposition of the matrix describing the spatial structure (e.g., the neighborhood matrix) was used to transform the CAR/SARrandomeffects into an independent, but heteroscedastic, Gaussian random effect. A linear predictor is fitted for the random effect variance to estimate the parameters in the CAR and SAR models. This gives a computationally efficient algorithm for moderately sized problems.

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 …

Working With Multilabel Datasets In R: The Mldr Package, Francisco Charte, David Charte

The R Journal

Most classification algorithms deal with datasets which have a set of input features, the variables to be used as predictors, and only one output class, the variable to be predicted. However, in late years many scenarios in which the classifier has to work with several outputs have come to life. Automatic labeling of text documents, image annotation or protein classification are among them. Multilabel datasets are the product of these new needs, and they have many specific traits. The mldr package allows the user to load datasets of this kind, obtain their characteristics, produce specialized plots, and manipulate them. The …

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 …

Apc: An R Package For Age-Period-Cohort Analysis, Bent Nielsen

The R Journal

The apc package includes functions for age-period-cohort analysis based on the canonical parametrisation of Kuang et al. (2008a). The package includes functions for organizing the data, descriptive plots, a deviance table, estimation of (sub-models of) the age-period-cohort model, a plot for specification testing, plots of estimated parameters, and sub-sample analysis.

News From The Bioconductor Project, The Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1104 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/. Navigate packages using ‘biocViews’ terms and title search. Each package has an html page with a description, links to vignettes, reference manuals, and usage statistics. Start using Bioconductor version 3.2 by installing R 3.2.3 and evaluating the commands

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.

Program Committee Report December 2015, Regenstrief Center For Healthcare Engineering

RCHE Reports

No abstract provided.

Effects Of Experience And Certification Level On Professional Development, Teacher Quality, And Increased Leadership Opportunities Of Nbcts, Jamie L. Burris

College of Education Dissertations

The focus of this dissertation was to provide insight into the perceptions of Arkansas National Board Certified Teachers (NBCTs) in regard to how the certification process impacted teaching and learning and overall student achievement. The purpose of this study was to determine the effects of experience and certification level on the perceptions of NBCTs in Arkansas concerning the quality of professional development earned, enhanced teacher quality, and increased leadership opportunities as a result of the National Board Certification process. An additional purpose of this study was to determine specifically how NBCTs perceived the certification process influenced student achievement within the …

Read 180 Participation, Ell Service Length, And Year On Literacy And Mathematics Achievement For Middle School Students, Paul A. Griep

College of Education Dissertations

The purpose of this dissertation was to add to the limited available research. In both hypotheses, the independent variables were whether or not the student used the READ 180 program, the number of years the student received ELL services in the United States (6 years or less or more than 6 years), and the year tested (2011 or 2012). The dependent variables for the first hypothesis were literacy and mathematics achievement measured by scaled scores obtained on the seventh grade Arkansas Augmented Benchmark Literacy and Mathematics examinations. The dependent variables for the second hypothesis were literacy and mathematics achievement measured …

Discourses On Time In The European Avant-Garde, Aaron Allen Hayes

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In the 1950s and 1960s, European composers, especially those interested in the development of serialism and electronic music, framed many of their aesthetic and compositional challenges as problems of time. This dissertation examines the writings and music of five notable composers from this era, and reconstructs the philosophical discourses that implicitly and explicitly provide the intellectual horizons for these temporal problems. In the late 1940s and early 1950s, Karlheinz Stockhausen, Karel Goeyvaerts, Pierre Boulez and Jean Barraqué attended the seminar offered by Olivier Messiaen at the Conservatoire National Supérior de Musique de Paris. With the exception of Barraqué, these composers …

Efficient Numerical Algorithms For Heterogeneous Computation Of Pde Extended Systems With Applications, Yiyang Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Partial Differential Equations (PDEs) and corresponding numerical schemes are explored to simulate scientific and engineering problems including parachute simulation and American option pricing. These problems involve appropriate coupling of several equations systems. A revised spring-mass model is used to describe the motion of parachute canopy and string motion which considers both string stiffness and angular stiffness. This model is validated by the material's Young's modulus and Poisson ratio and is proved to be convergent to continuum mechanics. The Navier-Stokes equation is applied to simulate the fluid field and a second-order accurate numerical scheme is used, together with the introduction of …

Structure Determination, Enzymatic Characterization, And Inhibitor Discovery Of Select Protein Targets Of Bacterial Pathogens, Brian Edward Mcgillick

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Our interests are in using structure based drug design to target bacterial agents and toxins that have the potential for intentional release into the environment and therefore pose a severe threat to public health and safety. Specifically, we focus on the pathogenic bacteria Francisella tularensis and Yersinia pestis, as well as the Clostridium botulinum neurotoxins (BoNTs). Our strategy for F. tularensis and Y. pestis was to target the bacterial system for fatty acid biosynthesis (FAS-II). The FAS-II system contains several enzymes whose sequence and structure is highly conserved across a vast array of pathogens. This coupled with the low homology …

Investigations Of Silver Vanadium Oxide And Silver Vanadium Phosphorous Oxide Solubility: Impact On Battery Performance, David Charles Bock

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Extended battery lifetime has increased impact with the prospect of long life applications such as electric vehicles and the integration of energy storage into the electric grid. Thus, consideration of parasitic reactions that occur over long periods of time has elevated significance. One such life limiting reaction for several battery systems is the dissolution of the cathode material into the battery electrolyte. This research investigates cathode solubility in the battery system used to power implantable cardioverter defibrillators (ICDs). The benchmark lithium/silver vanadium oxide (Ag2V4O11, SVO) system used in these devices has an unpredictable long term stability limitation attributed to cathode …

Minimally Disruptive Management Frameworks For Network Functions, Zafar Ayyub Qazi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Networks today rely on network functions or middleboxes (e.g. | firewalls, WAN optimizers) to provide critical performance, security, and policy compliance capabilities. However, today the management of these middleboxes is hard. First, these middleboxes are implemented as dedicated hardware appliances, making it difficult to dynamically scale resources. Second, operators need to carefully plan the network topology, manually set up rules to route traffic through the desired sequence of middleboxes, and implement safeguards for correct operation in the presence of failures and overload. We can overhaul today’s network infrastructure to address these problems by introducing flexibility in routing and the implementation …

Essays On Patent Licensing, Bruno Dutra Badia

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation consists of three essays dealing with issues related to patent licensing from a game-theoretic perspective. In the first essay, Chapter 2, the problem facing an inventor who holds the patent of a technology that can potentially be used to reduce the costs of firms in a given industry is considered. The technology's ability to cut firms' costs depends on a use for it being discovered, and the inventor has the option of trying or not to discover the use before licensing the technology to the firms. In this context, two main questions are addressed. First, which alternative should …

Indoor Localization And Tracking Using Binary Information, Li Geng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Real-time localization and tracking of people and assets within buildings is in high demand in many applications. These tasks are very challenging in indoor environments due to the physics of signal propagation and the multi-path interference. Satellite-based technologies such as the Global Positioning Systems (GPS) are notoriously unreliable in indoor environments. As a result, a variety of novel technologies have been developed to fill this gap. This dissertation focuses on the use of binary information for indoor localization and tracking, and in particular, on the use of the Ultra High Frequency (UHF) Radio Frequency Identification (RFID) technology. RFID is a …

From Sensor Networks To The Cloud: Smart System For Data Sensing, Matching And Storage, Ying Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

With the drastic growth of attention in crowed sensing and wireless based social network applications, it is in desperate need to establish a comprehensive infrastructure that can efficiently sense the data, then accurately matches and delivers the gathered information to the various parties of interests in a timely manner. On the other end of the picture, the huge amount of user data needs to be reliably stored with easy and fast access at anytime and from anywhere. These inter-connected challenging problems form a complete information service framework of my thesis. In this thesis, we first introduce a set of adaptive …

Exact Results In Supersymmetric And Superconformal Quantum Field Theories, Wolfger Peelaers

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation we perform exact, non-perturbative computations in supersymmetric and superconformal quantum field theories. In the first part, we show that the conformal bootstrap equations, which implement the requirement that in a conformal quantum field theory any four-point function should be crossing symmetric, have an exactly solvable truncation in theories with extended supersymmetry. As a result, we introduce a new 4d/2d correspondence that assigns to any four-dimensional N =2 superconformal quantum field theory, Lagrangian or non-Lagrangian, a two-dimensional chiral algebra, and subsequently explore its structure in the context of theories of class S. In the second part, we extend …

Multi-Marker Linkage Disequilibrium Mapping Of Quantitative Trait Loci, Soyoun Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Background: Genome-wide associations have been studied for years to infer relationships between biological traits and their underlying genetic causes, known as quantitative traits loci (QTL), in a process known as QTL mapping. Single nucleotide polymorphisms (SNPs), which are commonly used genetic markers, are usually in linkage disequilibrium (LD) with each other within a small genetic region. Both single- and double-marker-based LD mapping methods have been developed by taking advantage of LD structure. Method: In this thesis, a more general LD mapping framework with an arbitrary number of markers has been developed in order to improve LD mapping and its detection …