Numerical Analysis and Scientific Computing Commons^™

Contact Process On Generalized Fibonacci Chains: Infinite-Modulation Criticality And Double-Log Periodic Oscillations, Hatem Barghathi, David Nozadze, Thomas Vojta

Physics Faculty Research & Creative Works

We study the nonequilibrium phase transition of the contact process with aperiodic transition rates using a real-space renormalization group as well as Monte Carlo simulations. The transition rates are modulated according to the generalized Fibonacci sequences defined by the inflation rules A → AB^k and B → A. For k=1 and 2, the aperiodic fluctuations are irrelevant, and the nonequilibrium transition is in the clean directed percolation universality class. For k ≥ 3, the aperiodic fluctuations are relevant. We develop a complete theory of the resulting unconventional "infinite-modulation" critical point, which is characterized by activated dynamical scaling. Moreover, observables …

Dynamical (E,2e) Studies Of Tetrahydropyran And 1,4-Dioxane, J. D. Builth-Williams, G. Da Silva, L. Chiari, D. B. Jones, Hari Chaluvadi, Don H. Madison, M. J. Brunger

Physics Faculty Research & Creative Works

We present experimental and theoretical results for the electron-impact ionization of the highest occupied molecular orbitals of tetrahydropyran and 1,4-dioxane. Using an (e,2e) technique in asymmetric coplanar kinematics, angular distributions of the slow ejected electron, with an energy of 20 eV, are measured when incident electrons at 250 eV ionize the target and scatter through an angle of either -10° or -15°. The data are compared with calculations performed at the molecular 3-body distorted wave level. Fair agreement between the theoretical model and the experimental measurements was observed. The similar structures for these targets provide key insights for assessing the …

Kapitza Resistance Of Si/Sio₂ Interface, Bowen Deng, Aleksandr V. Chernatynskiy, Marat Khafizov, David H. Hurley, Simon R. Phillpot

Physics Faculty Research & Creative Works

A phonon wave packet dynamics method is used to characterize the Kapitza resistance of a Si/SiO₂ interface in a Si/SiO₂/Si heterostructure. By varying the thickness of SiO₂ layer sandwiched between two Si layers, we determine the Kapitza resistance for the Si/SiO ₂ interface from both wave packet dynamics and a direct, non-equilibrium molecular dynamics approach. The good agreement between the two methods indicates that they have each captured the anharmonic phonon scatterings at the interface. Moreover, detailed analysis provides insights as to how individual phonon mode scatters at the interface and their contribution to the Kapitza …

Phonon Thermal Transport Through Tilt Grain Boundaries In Strontium Titanate, Zexi Zheng, Xiang Chen, Bowen Deng, Aleksandr V. Chernatynskiy, Shengfeng Yang, Jinjun Xiong, Youping Chen

Physics Faculty Research & Creative Works

In this work, we perform nonequilibrium molecular dynamics simulations to study phonon scattering at two tilt grain boundaries (GBs) in SrTiO₃. Mode-wise energy transmission coefficients are obtained based on phonon wave-packet dynamics simulations. The Kapitza conductance is then quantified using a lattice dynamics approach. The obtained results of the Kapitza conductance of both GBs compare well with those obtained by the direct method, except for the temperature dependence. Contrary to common belief, the results of this work show that the optical modes in SrTiO₃ contribute significantly to phonon thermal transport, accounting for over 50% of the Kapitza …

Strong-Randomness Infinite-Coupling Phase In A Random Quantum Spin Chain, Fawaz Hrahsheh, José A. Hoyos, Rajesh Narayanan, Thomas Vojta

Physics Faculty Research & Creative Works

We study the ground-state phase diagram of the Ashkin-Teller random quantum spin chain by means of a generalization of the strong-disorder renormalization group. In addition to the conventional paramagnetic and ferromagnetic (Baxter) phases, we find a partially ordered phase characterized by strong randomness and infinite coupling between the colors. This unusual phase acts, at the same time, as a Griffiths phase for two distinct quantum phase transitions, both of which are of infinite-randomness type. We also investigate the quantum multicritical point that separates the two-phase and three-phase regions, and we discuss generalizations of our results to higher dimensions and other …

A Comparative Study Of Reservoir Computing For Temporal Signal Processing, Alireza Goudarzi, Peter Banda, Matthew R. Lakin, Christof Teuscher, Darko Stefanovic

Computer Science Faculty Publications and Presentations

Reservoir computing (RC) is a novel approach to time series prediction using recurrent neural networks. In RC, an input signal perturbs the intrinsic dynamics of a medium called a reservoir. A readout layer is then trained to reconstruct a target output from the reservoir's state. The multitude of RC architectures and evaluation metrics poses a challenge to both practitioners and theorists who study the task-solving performance and computational power of RC. In addition, in contrast to traditional computation models, the reservoir is a dynamical system in which computation and memory are inseparable, and therefore hard to analyze. Here, we compare …

The R Journal (December 2013) 5(2): Complete Issue, The R Foundation

The R Journal

Editorial, Hadley Wickham

Contributed Research Articles

factorplot: Improving Presentation of Simple Contrasts in Generalized Linear Models, David A. Armstrong II

spMC: Modelling Spatial Random Fields with Continuous Lag Markov Chains, Luca Sartore

RNetCDF: A Package for Reading and Writing NetCDF Datasets, Pavel Michna and Milton Woods

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

Performance Attribution for Equity Portfolios, Yang Lu and David Kane

ExactCIdiff: An R Package for Computing Exact Confidence Intervals for the Difference of Two Proportions, Guogen Shan and Weizhen Wang

rlme: An R Package for Rank-Based Estimation and Prediction in Random …

Short-Term Inflation Forecasting Models For Nigeria, Sani I. Doguwa, Sarah O. Alade

CBN Journal of Applied Statistics (JAS)

Short-term inflation forecasting is an essential component of the monetary policy projections at the Central Bank of Nigeria. This paper proposes four short-term headline inflation forecasting models using the SARIMA and SARIMAX processes and compares their performance using the pseudo-out-of-sample forecasting procedure over July 2011 to September 2013. According to the results the best forecasting performance is demonstrated by the model based on the all items CPI estimated using the SARIMAX model. This model is, therefore, recommended for use in short-term forecasting of headline inflation in Nigeria. The forecasting performance up to eight months ahead, of the models based on …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

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.