Computer Sciences Commons^™

Correspondence Analysis On Generalised Aggregated Lexical Tables (Ca-Galt) In The Factominer Package, Belchin Kostov, Mónica Bécue-Bertaut, François Husson

The R Journal

Correspondence analysis on generalised aggregated lexical tables (CA-GALT) is a method that generalizes classical CA-ALT to the case of several quantitative, categorical and mixed variables. It aims to establish a typology of the external variables and a typology of the events from their mutual relationships. In order to do so, the influence of external variables on the lexical choices is untangled cancelling the associations among them, and to avoid the instability issued from multicollinearity, they are substituted by their principal components. The CaGalt function, implemented in the FactoMineR package, provides numerous numerical and graphical outputs. Confidence ellipses are also provided …

Rdrobust: An R Package For Robust Nonparametric Inference In Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, Rocío Titiunik

The R Journal

This article describes the R package rdrobust, which provides data-driven graphical and in ference procedures for RD designs. The package includes three main functions: rdrobust, rdbwselect and rdplot. The first function (rdrobust) implements conventional local-polynomial RD treatment effect point estimators and confidence intervals, as well as robust bias-corrected confidence intervals, for average treatment effects at the cutoff. This function covers sharp RD, sharp kink RD, fuzzy RD and fuzzy kink RD designs, among other possibilities. The second function (rdbwselect) implements several bandwidth selectors proposed in the RD literature. The third function (rdplot) provides data-driven optimal choices of evenly-spaced and …

News From The Bioconductor Project, Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1024 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 3.1 by installing R 3.2.1 and evaluating the commandS

Implementing Persistent O(1) Stacks And Queues In R, Shawn T. O'Neil

The R Journal

True to their functional roots, most R functions are side-effect-free, and users expect datatypes to be persistent. However, these semantics complicate the creation of efficient and dynamic data structures. Here, we describe the implementation of stack and queue data structures satisfying these conditions in R, available in the CRAN package rstackdeque. Guided by important work in purely functional languages, we look at both partially- and fully-persistent versions of queues, comparing their performance characteristics. Finally, we illustrate the usefulness of such dynamic structures with examples of generating and solving mazes.

Showtext: Using System Fonts In R Graphics, Yixuan Qiu

The R Journal

This article introduces the showtext package that makes it easy to use system fonts in R graphics. Unlike other methods to embedfonts into graphics, showtext converts text into raster images or polygons, and then adds them to the plot canvas. This method produces platform-independent image files that do not rely on the fonts that create them. It supports a large number of font formats and Rgraphics devices, and meanwhile provides convenient features such as using web fonts and integrating with knitr. This article provides an elaborate introduction to the showtext package, including its design, usage, and examples.

Editorial, Bettina Grün

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 7, Issue 1 of the R Journal. This issue contains 16 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small insight into the wide variety of functionality covered currently by the more than 6800 packages available from CRAN.

Manipulation Of Discrete Random Variables With Discreterv, Eric Hare, Andreas Buja, Heike Hofmann

The R Journal

A prominent issue in statistics education is the sometimes large disparity between the theoretical and the computational coursework. discreteRV is an R package for manipulation of discrete random variables which uses clean and familiar syntax similar to the mathematical notation in introductory probability courses. The package offers functions that are simple enough for users with little experience with statistical programming, but has more advanced features which are suitable for a large number of more complex applications. In this paper, we introduce and motivate discreteRV, describe its functionality, and provide reproducible examples illustrating its use.

The Complex Multivariate Gaussian Distribution, Robin K.S. Hankin

The R Journal

Here I introduce package cmvnorm, a complex generalization of the mvtnorm package. A complex generalization of the Gaussian process is suggested and numerical results presented using the package. An application in the context of approximating the Weierstrass-function using a complex Gaussian process is given.

Dietary Microrna Database (Dmd): An Archive Database And Analytic Tool For Food-Borne Micrornas, Kevin Chiang, Jiang Shu, Janos Zempleni, Juan Cui

School of Computing: Faculty Publications

With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental …

Robust And Real-Time Stereo Matching On Parallel Graphics Hardware Using Gradient-Based Disparity Refinement, Jedrzej Kowalczuk

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Computer vision attempts to provide camera-equipped machines with visual perception, i.e., the capability to comprehend their surroundings through the analysis and understanding of images. The ability to perceive depth is a vital component of visual perception that enables machines to interpret the three-dimensional structure of their surroundings and allows them to navigate through the environment. In computer vision, depth perception is achieved via stereo matching, a process that identifies correspondences between pixels in images acquired using a pair of horizontally offset cameras. It is possible to calculate depths from correspondences or, more specifically, the positional offsets (disparities) between pixels in …

Reflective, Deliberative Agent-Based Information Gathering, Adam D. Eck

School of Computing: Dissertations, Theses, and Student Research

As computational devices and entities become further established as routine, omnipresent components of our everyday lives (e.g., wearable sensors, smart homes, cyber-physical systems, embodied agents, human-robot interactions), such systems face an increased pressure to perpetually understand the complex, noisy, uncertain world around them in real-time. This environmental knowledge enables computational systems to intelligently decide how to best behave in response to the current situation, adapt to the ever-changing conditions of the dynamic world, and accomplish system goals that ultimately aim to improve our daily experience. However, achieving and maintaining such knowledge is very complicated due to the complexities and challenging …

Visual Analytics For Large Communication Trace Data, Jieting Wu

School of Computing: Dissertations, Theses, and Student Research

Executions of modern parallel programs often yield complex communications among compute nodes of large-scale clusters of workstations or supercomputers. Analyzing communication patterns is becoming increasingly critical to performance optimiza- tion. As the scale and complexity of parallel applications drastically increases, visu- alization has become a feasible means to conduct analysis of massive communication patterns. However, most visualization tools fall short in showing comprehensive dy- namic communication graph and addressing the scalability issue. Our solution for analyzing dynamic communication patterns is based on an analytics framework cou- pled with a new visualization technique, named CommGram [29], that provides a flexible solution …

Developing An Image-Based Classifier For Detecting Poetic Content In Historic Newspaper Collections, Elizabeth M. Lorang, Leen-Kiat Soh, Maanas Varma Datla, Spencer Kulwicki

University of Nebraska-Lincoln Libraries: Faculty Publications

"Developing an Image-Based Classifier for Detecting Poetic Content in Historic Newspaper Collections" details and analyzes the first stage of work of the Image Analysis for Archival Discovery project team. Our team is is investigating the use of image analysis to identify poetic content in historic newspapers. The project seeks both to augment the study of literary history by drawing attention to the magnitude of poetry published in newspapers and by making the poetry more readily available for study, as well as to advance work on the use of digital images in facilitating discovery in digital libraries and other digitized collections. …

Clustering Header Categories Extracted From Web Tables, George Nagy, David W. Embley, Mukkai Krishnamoorthy, Sharad C. Seth

School of Computing: Conference and Workshop Papers

Revealing related content among heterogeneous web tables is part of our long term objective of formulating queries over multiple sources of information. Two hundred HTML tables from institutional web sites are segmented and each table cell is classified according to the fundamental indexing property of row and column headers. The categories that correspond to the multi-dimensional data cube view of a table are extracted by factoring the (often multi-row/column) headers. To reveal commonalities between tables from diverse sources, the Jaccard distances between pairs of category headers (and also table titles) are computed. We show how about one third of our …

A Middleware Framework For Application-Aware And User-Specific Energy Optimization In Smart Mobile Devices, Sudeep Pasricha, Brad K. Donohoo, Chris Ohlsen

United States Air Force: Publications

munication, and social interaction. In addition to the demand for an acceptable level of performance and a comprehensive set of features, users often desire extended battery lifetime. In fact, limited battery lifetime is one of the biggest obstacles facing the current utility and future growth of increasingly sophisticated ‘‘smart’’ mobile devices. This paper proposes a novel application-aware and user-interaction aware energy optimization middleware framework (AURA) for pervasive mobile devices. AURA optimizes CPU and screen backlight energy consumption while maintaining a minimum acceptable level of performance. The proposed framework employs a novel Bayesian application classifier and management strategies based on Markov …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

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 934 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/release/. 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 and R version 3.1

Changes In R, The R Core Team

The R Journal

CHANGES IN 3.1.2

R Foundation News, Martin Mächler, Kurt Hornik

The R Journal

New R Foundation board

New ordinary members

Donations and new supporting members

Conference Report Polish Academic R User Meeting, Maciej Beręsewicz, Alicja Szabelska, Joanna Zyprych-Walczak, Łukasz Wawrowski

The R Journal

The first national conference “Polish Academic R User Meeting” (PAZUR) was held at the Poznan University of Economics from October 15–17, 2014. The organizers of the conference were the Department of Statistics at the Poznan University of Economics (PUE), the Department of Mathematical and Statistical Methods at the Poznan University of Life Sciences (PULS) and SKN Estymator, the students scientific association that resides at the Department of Statistics at the Poznan University of Economics. The honorary patronage of the conference took Professor Emil Panek, Dean of the Faculty of Informatics and Electronic Economy PUE and Professor Wiesław Koziara, Dean of …

Conference Report: R In Insurance 2014, Markus Gesmann, Andreas Tsanakas

The R Journal

The 2nd Rin Insurance conference took place at Cass Business School London on 14 July 2014. This one-day conference focused once more on the wide range of applications of Rin insurance, actuarial science and beyond. The conference programme covered topics including reserving, pricing, loss modelling, the use of R in a production environment and muchmore.

Qmethod: A Package To Explore Human Perspectives Using Q Methodology, Aiora Zabala

The R Journal

Q is a methodology to explore the distinct subjective perspectives that exist within a group. It is used increasingly across disciplines. The methodology is semi-qualitative and the data are analysed using data reduction methods to discern the existing patterns of thought. This package is the first to perform Q analysis in R, and it provides many advantages to the existing software: namely, it is fully cross-platform, the algorithms can be transparently examined, it provides results in a clearly structured and tabulated form ready for further exploration and modelling, it produces a graphical summary of the results, and it generates a …

Farewell's Linear Increments Model For Missing Data: The Flim Package, Rune Hoff, Jon Michael Gran, Daniel Farewell

The R Journal

Missing data is common in longitudinal studies. We present a package for Farewell’s Linear Increments Model for Missing Data (the FLIM package), which can be used to fit linear models for observed increments of longitudinal processes and impute missing data. The method is valid for data with regular observation patterns. The end result is a list of fitted models and a hypothetical complete dataset corresponding to the data we might have observed had individuals not been missing. The FLIM package may also be applied to longitudinal studies for causal analysis, by considering counterfactual data as missing data- for instance to …

Smr: An R Package For Computing The Externally Studentized Normal Midrange Distribution, Ben Dêivide, Oliveira Batista, Daniel Furtado Ferreira

The R Journal

The main purpose of this paper is to present the main algorithms underlining the con struction and implementation of the SMR package, whose aim is to compute studentized normal midrange distribution. Details on the externally studentized normal midrange and standardized normal midrange distributions are also given. The package follows the same structure as the prob ability functions implemented in R. That is: the probability density function (dSMR), the cumulative distribution function (pSMR), the quantile function (qSMR) and the random number generating function (rSMR). Pseudocode and illustrative examples of how to use the package are presented.

Sgof: An R Package For Multiple Testing Problems, Irene Castro-Conde, Jacob De Uña-Álvarez

The R Journal

In this paper we present a new R package called sgof for multiple hypothesis testing. The principal aim of this package is to implement SGoF-type multiple testing methods, known to be more powerful than the classical false discovery rate (FDR) and family-wise error rate (FWER) based methods in certain situations, particularly when the number of tests is large. This package includes Bi nomial and Conservative SGoF and the Bayesian and Beta-Binomial SGoF multiple testing procedures, which are adaptations of the original SGoF method to the Bayesian setting and to possibly correlated tests, respectively. The sgof package also implements the Benjamini-Hochberg …

Flexible R Functions For Processing Accelerometer Data, With Emphasis On Nhanes 2003–2006, Dane R. Van Domelen, W. Stephen Pittard

The R Journal

Accelerometers are a valuable tool for measuring physical activity (PA) in epidemiological studies. However, considerable processing is needed to convert time-series accelerometer data into meaningful variables for statistical analysis. This article describes two recently developed R packages for processing accelerometer data. The package accelerometry contains functions for performing various data processing procedures, such as identifying periods of non-wear time and bouts of activity. The functions are flexible, computationally efficient, and compatible with uniaxial or triaxial data. The package nhanesaccel is specifically for processing data from the National Health and Nutrition Examination Survey (NHANES), years 2003–2006. Its primary function generates measures …

Automatic Conversion Of Tables To Longform Dataframes, Jimmy Oh

The R Journal

TableToLongForm automatically converts hierarchical Tables intended for a human reader into a simple LongForm dataframe that is machine readable, making it easier to access and use the data for analysis. It does this by recognising positional cues present in the hierarchical Table (which would normally be interpreted visually by the human brain) to decompose, then reconstruct the data into a LongForm dataframe. The article motivates the benefit of such a conversion with an example Table, followed by a short user manual, which includes a comparison between the simple one argument call to TableToLongForm, with code for an equivalent manual conversion. …

Gset: An R Package For Exact Sequential Test Of Equivalence Hypothesis Based On Bivariate Non-Central T-Statistics, Fang Liu

The R Journal

The R package gset calculates equivalence and futility boundaries based on the exact bivariate non-central t test statistics. It is the first R package that targets specifically at the group sequential test of equivalence hypotheses. The exact test approach adopted by gset neither assumes the large-sample normality of the test statistics nor ignores the contribution to the overall Type I error rate from rejecting one out of the two one-sided hypotheses under a null value. The features of gset include: error spending functions, computation of equivalence boundaries and futility boundaries, either binding or nonbinding, depiction of stagewise boundary plots, and …

Editorial, Deepayan Sarkar

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 6, Issue 2 of the R Journal.

Mvn: An R Package For Assessing Multivariate Normality, Selcuk Korkmaz, Dincer Goksuluk, Gokmen Zararsiz

The R Journal

Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as MANOVA, linear discriminant analysis, principal component analysis, canonical correlation, etc. It is important to assess multivariate normality in order to proceed with such statistical methods. There are many analytical methods proposed for checking multivariate normality. However, deciding which method to use is a challenging process, since each method may give different results under certain conditions. Hence, we may say that there is no best method, which is valid under any condition, for normality checking. In addition to numerical results, it is very useful to …