Digital Commons Network^™

Conference Report: Deuxièmes Rencontres R, Aurelie Siberchicot, Stephane Dray

The R Journal

Following the success of the first "Rencontres R" (Bordeaux, 2-3 July 2012, http://r2012. bordeaux.inria.fr/), the second meeting was held in Lyon on 27-28 June 2013. This French speaking conference was a great success with 216 participants (110 were present at the first conference). The aim of the meeting was to provide a national forum for the exchange and sharing of ideas on the use of R in different disciplines. The number of participants and the list of sponsors (http://r2013-lyon.sciencesconf.org/resource/sponsors) demonstrate the increasing impact of R in both industry and academia in France. The program, detailed below, consisted of plenary sessions, …

News From The Bioconductor Project, Bioconductor Team

The R Journal

Bioconductor 2.13 was released on 15 October2013. It is compatible with R3.0.2, and consists of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages. The release includes 84 new software packages, and enhancements to many others. Descriptions of new packages and updated NEWS files provided by current package maintainers are at http://bioconductor.org/news/bioc_2_13_release/

Complognormal: An R Package For Composite Lognormal Distributions, S. Nadarajah, S. A.A. Bakar

The R Journal

In recent years, composite models based on the lognormal distribution have become popular in actuarial sciences and related areas. In this short note, we present a new R package for computing the probability density function, cumulative density function, and quantile function, and for generating random numbersof anycomposite model based on the lognormal distribution. The use of the package is illustrated using a real data set.

Dynamic Parallelization Of R Functions, Stefan Böhringer

The R Journal

R offers several extension packages that allow it to perform parallel computations. These operate on fixed points in the program flow and make it difficult to deal with nested parallelism and to organize parallelism in complex computations in general. In this article we discuss, first, of how to detect parallelism in functions, and second, how to minimize user intervention in that process. We present a solution that requires minimal code changes and enables to flexibly and dynamically choose the degree of parallelization in the resulting computation. An implementation is provided by the R package parallelize.dynamic and practical issues are discussed …

Surface Melting Curve Analysis With R, Stefan Rödiger, Alexander Böhm, Ingolf Schimke

The R Journal

Nucleic acid Melting Curve Analysis is a powerful method to investigate the interaction of double stranded nucleic acids. Many researchers rely on closed source software which is not ubiquitously available, and gives only little control over the computation and data presentation. R in contrast, is open source, highly adaptable and provides numerous utilities for data import, sophisticated statistical analysis and presentation in publication quality. This article covers methods, implemented in the MBmca package, for DNA Melting Curve Analysis on microbead surfaces. Particularly, the use of the second derivative melting peaks is suggested as an additional parameter to characterize the melting …

Factorplot: Improving Presentation Of Simple Contrasts In Generalized Linear Models, David A. Armstrong Ii

The R Journal

Recent statistical literature has paid attention to the presentation of pairwise comparisons either from the point of view of the reference category problem in generalized linear models (GLMs) or in terms of multiple comparisons. Both schools of thought are interested in the parsimonious presentation of sufficient information to enable readers to evaluate the significance of contrasts resulting from the inclusion of qualitative variables in GLMs. These comparisons also arise when trying to interpret multinomial models where one category of the dependent variable is omitted as a reference. While considerable advances have been made, opportunities remain to improve the presentation of …

Changes In R, The R Core Team

The R Journal

CHANGES IN R 3.0.2

R Foundation News, Kurt Hornik

The R Journal

Donations and new members

• Donations
• New supporting institutions
• New supporting members

The R In Robotics, André Dietrich, Sebastian Zug, Jörg Kaiser

The R Journal

The aim of this contribution is to connect two previously separated worlds: robotic application development with the Robot Operating System (ROS) and statistical programming with R. This fruitful combination becomes apparent especially in the analysis and visualization of sensory data. We therefore introduce a new language extension for ROS that allows to implement nodes in pure R. All relevant aspects are described in a step-by-step development of a common sensor data transformation node. This includes the reception of raw sensory data via the ROS network, message interpretation, bag-file analysis, transformation and visualization, as well as the transmission of newly generated …

Spmc: Modelling Spatial Random Fields With Continuous Lag Markov Chains, Luca Sartore

The R Journal

Currently, a part of the R statistical software is developed in order to deal with spatial models. More specifically, some available packages allow the user to analyse categorical spatial random patterns. However, only the spMC package considers a viewpoint based on transition probabilities between locations. Through the use of this package it is possible to analyse the spatial variability of data, make inference, predict and simulate the categorical classes in unobserved sites. An example is presented by analysing the well-known Swiss Jura data set.

Rlme: An R Package For Rank-Based Estimation And Prediction In Random Effects Nested Models, Yusuf K. Bilgic, Herbert Susmann

The R Journal

There is a lack of robust statistical analyses for random effects linear models. In practice, statistical analyses, including estimation, prediction and inference, are not reliable when data are unbalanced, of small size, contain outliers, or not normally distributed. It is fortunate that rank-based regression analysis is a robust nonparametric alternative to likelihood and least squares analysis. We propose an R package that calculates rank-based statistical analyses for two- and three-level random effects nested designs. In this package, a new algorithm which recursively obtains robust predictions for both scale and random effects is used, along with three rank-based fitting methods.

Performance Attribution For Equity Portfolios, Yang Lu, David Kane

The R Journal

The pa package provides tools for conducting performance attribution for long-only, single currency equity portfolios. The package uses two methods: the Brinson-Hood-Beebower model (hereafter referred to as the Brinson model) and a regression-based analysis. The Brinson model takes an ANOVA-type approach and decomposes the active return of any portfolio into asset allocation, stock selection, and interaction effect. The regression-based analysis utilizes estimated coefficients, based on a regression model, to attribute active return to different factors.

Temporal Disaggregation Of Time Series, Christoph Sax, Peter Steiner

The R Journal

Temporal disaggregation methods are used to disaggregate low frequency time series to higher frequency series, where either the sum, the average, the first or the last value of the resulting high frequency series is consistent with the low frequency series. Temporal disaggregation can be performed with or without one or more high frequency indicator series. The package tempdisagg is a collection of several methods for temporal disaggregation.

On Sampling From The Multivariate T Distribution, Marius Hofert

The R Journal

The multivariate normal and the multivariate t distributions belong to the most widely used multivariate distributions in statistics, quantitative risk management, and insurance. In contrast to the multivariate normal distribution, the parameterization of the multivariate t distribution does not correspond to its moments. This, paired with a non-standard implementation in the R package mvtnorm, provides traps for working with the multivariate t distribution. In this paper, common traps are clarified and corresponding recent changes to mvtnorm are presented.

Editorial, Hadley Wickham

The R Journal

Welcome to volume 5, issue 2 of The R Journal. I’m very pleased to include 21 articles about R for your enjoyment.

The end of the year also brings changes to the editorial board. Martyn Plummer is leaving the board after four years. Martyn was responsible for writing up the standard operating procedures for the journal, an act which has made my life as a new editor considerably easier! We welcome Michael Lawrence, who will join the editorial board in 2014. I am stepping down as Editor-in-Chief and will be leaving this task in the capable hands of Deepayan Sarkar.

Rnetcdf: A Package For Reading And Writing Netcdf Datasets, Pavel Michna, Milton Woods

The R Journal

This paper describes the RNetCDF package (version 1.6), an interface for reading and writing files in Unidata NetCDF format, and gives an introduction to the NetCDF file format. NetCDF is a machine independent binary file format which allows storage of different types of array based data, along with short metadata descriptions. The package presented here allows access to the most important functions of the NetCDF C-interface for reading, writing, and modifying NetCDF datasets. In this paper, we present a short overview on the NetCDF file format and show usage examples of the package.

Betategarch: Simulation, Estimation And Forecasting Of Beta-Skew-T-Egarch Models, Genaro Sucarrat

The R Journal

This paper illustrates the usage of the betategarch package, a package for the simulation, estimation and forecasting of Beta-Skew-t-EGARCH models. The Beta-Skew-t-EGARCH model is a dynamic model of the scale or volatility of financial returns. The model is characterised by its robustness to jumps or outliers, and by its exponential specification of volatility. The latter enables richer dynamics, since parameters need not be restricted to be positive to ensure positivity of volatility. In addition, the model also allows for heavy tails and skewness in the conditional return (i.e. scaled return), and for leverage and a time-varying long-term component in the …

Lfe: Linear Group Fixed Effects, Simen Gaure

The R Journal

Linear models with fixed effects and many dummy variables are common in some fields. Such models are straightforward to estimate unless the factors have too many levels. The R package lfe solves this problem by implementing a generalization of the within transformation to multiple factors, tailored for large problems.

Changes To Grid For R 3.0.0, Paul Murrell

The R Journal

From R 3.0.0, there is a new recommended way to develop new grob classes in grid. In a nutshell, two new “hook” functions, makeContext() and makeContent() have been added to grid to provide an alternative to the existing hook functions preDrawDetails(), drawDetails(), and postDrawDetails(). There is also a new function called grid.force(). This article discusses why these changes have been made, provides a simple demonstration of the use of the new functions, and discusses some of the implications for packages that build on grid.

Exactcidiff: An R Package For Computing Exact Confidence Intervals For The Difference Of Two Proportions, Guogen Shan, Weizhen Wang

The R Journal

Comparing two proportions through the difference is a basic problem in statistics and has applications in many fields. More than twenty confidence intervals (Newcombe, 1998a,b) have been proposed. Most of them are approximate intervals with an asymptotic infimum coverage probability much less than the nominal level. In addition, large sample may be costly in practice. So exact optimal confidence intervals become critical for drawing valid statistical inference with accuracy and precision. Recently, Wang (2010, 2012) derived the exact smallest (optimal) one-sided 1 confidence intervals for the difference of two paired or independent proportions. His intervals, however, are computer-intensive by nature. …

Parenting Skills As Predictors Of Child And Adolescent Psychotherapy Outcomes: Examining Change In Usual Care Settings, Alicia Ann Henderson

Theses and Dissertations

Youth psychotherapy literature is in need of more research related to understanding psychotherapy process and outcome in child psychotherapy in community settings. The purpose of this study was to examine how key parenting skills were associated with child and adolescent symptoms and outcomes over the course of treatment in an outpatient community mental health system. Much of the research on child and adolescent outcomes has been conducted in controlled research settings, which raises the importance of more research needing to be done in representative clinical practice conditions (Weisz & Jensen, 2001). Further, few child and adolescent studies have examined potential …

Ferritin-Based Photo-Oxidation Of Biomass For Nanoparticle Synthesis, Bioremediation, And Hydrogen Evolution, Oscar Petrucci

Theses and Dissertations

The cell is the basic unit of all living organisms. It is an amazing machine capable of self-replicating, growing, and synthesizing and shuttling thousands of compounds. To perform all of these activities the cell needs energy. The original source of energy for all living beings is the Sun. The energy of the sun is collected by the autotrophs (mostly plants) through photosynthesis and stored in the chemical bonds of carbohydrates and lipids through carboxylic acid intermediates; animals use these compounds to obtain the energy for their cells. Most of the energy extracted by the cell comes from the citric acid …

Algorithms For The Implementation Of A Dynamic Energy Pricing Policy, Manek Biswas

Theses - ALL

In the upcoming smart grid era, dynamic pricing using primarily data collected from smart meters installed in homes and businesses is a virtual certainty. The possibilities this feature may offer are many, and we examine in this study how subunits of the electricity grid may implement load scheduling given a model for predicting ever-changing energy prices over a day. We present a realistic linear model that utilities may use for implementing dynamic pricing, and argue how accurate prediction of this model by its customers may be profitable both for the utilities and their customers.

The thesis provides algorithms for achieving …

Nature Of Science Conceptions, Attitudes Towards Evolution And Global Climate Change, And Course Achievement In An Introductory Biology Course, Benjamin Elijah Carter

Theses - ALL

Many researchers have studied student attitudes toward and knowledge of evolutionary science, attitudes towards global climate change (GCC), conceptions about the nature of science (NOS), and course success. However, at the time of this writing, no studies explicitly link these topics.

It is overwhelmingly acknowledged by the scientific community that evolution and global climate change (GCC) are undeniably supported by physical evidence. And yet, both topics remain very politically contentious in the United States. Efforts to mitigate the disconnects between the scientific community and the general public on these issues are imperative to science education. Such undertakings need to examine …

A Study On Two Optimal Planning Problems In Smart Grid, Eting Yuan

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

Optimized planning of power devices and power generators is essential for saving energy and reducing costs in smart grid. Many of these optimization problems share a common characteristic and seek to optimize accumulated rewards or costs within a finite time planning horizon. For this reason, some of those problems can be formulated as finite horizon optimal planning problems. This dissertation performs detailed investigation on two representative finite horizon optimal planning problems: the Unit Commitment problem (UCP) and the Voltage and Reactive Power Control (VVC) Problem. UCP is an important optimal power planning problems in electric grids. The purpose of UCP …

Energy Performance Evaluation And Energy Savings Opportunities For Manufacturing Systems, Shiyao Wang

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

Presently, with the development of modern manufacturing system, the usage of energy is growing rapidly. Since most of fuel we use are non-renewable resources, fuel becomes a very big part of cost. How to use the energy more efficiently is the main concern now. This thesis provides a systematic method to evaluate the energy efficiency of a production system and decompose the unnecessary energy waste of a manufacturing facility from the measured data with stochastic frontier analysis model. A new energy efficiency indicator is developed for the energy consumption level and efficiency of machines and production lines. Energy savings opportunity …

Computer Aided Design Of Planar Four-Bar Linkages On Ios Using A Novel Svd Algorithm, Xin Ge

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

Motion synthesis has been a practical topic existing for a long time. Various methods have been tried and put into practice. It is well done by the scientists and engineers to solve large equations of matrix. Although it can be done and get the good result, the efficiency is low and labor is very much consuming. Comparatively, our methods are much more easier and efficient, it is more suitable for the software to realize the calculation by itself. It is mature in PCs to have a motion synthesis software, but since the mobile system is going into everyday life and …

A Distributed Mac Protocol For Efficient Channelization In Wireless Networks, Seyed Kaveh Fayazbakhsh

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

There is a significant interest in designing new wireless multiple access protocols that split a wide frequency channel into multiple sub-channels and assign these sub-channels to competing transmissions. Doing this adaptively depending on the number of competing transmissions has a tremendous potential both in high-speed and white-space networks. While such protocols have been developed, they suffer from limitations such as considerable protocol overheads, dependence on a centralized controller, and assumptions about the network being static, etc. In this work, we develop a new multiple access protocol, Ez-Channel, that adaptively and efficiently channelizes the spectrum for improving throughput, without encountering the …

The Dynamical Basis Of The Decanalization Of Gene Expression In Kr Uppel Mutant Embryos, Lena Panok

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

Canalization is the ability of an organism's phenotype to remain stable under a perturbation in their genotype or the environment. It has been noted that there is no canalization or canalization is to a much smaller degree in mutants than in wild type. Waddington's idea was to understand canalization through studying gene interactions. We investigate the mechanisms of canalization of gap gene patterns in D.melanogaster through dynamical analysis of the gene circuit. To carry out this investigation we construct a dynamical model of the evolution of the concentration of protein products of the gap genes in time. Our model, which …

Scalable Particle And Mesh Algorithms For Elliptic Components Of Multiphase Problems, Tongfei Guo

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

New mesh and meshless algorithms for elliptic boundary and elliptic interface problems have been developed. By utilizing the embedded boundary method, a mesh based algorithm to solve elliptic interface problem is implemented as an extension of hybrid Eulerian-Lagrangian hydrodynamic library FronTier which employs the method of front tracking for interface propagation and this implementation is parallelized for distributed memory clusters. The use of embedded boundary method supports arbitrary discontinuities of density and other physics properties across the interfaces and significantly improves methods that smear interface discontinuities across several grid cells. This code has been applied to process simulation for heat …