Numerical Analysis and Scientific Computing Commons^™

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.

An Immersive Telepresence System Using Rgb-D Sensors And Head-Mounted Display, Xinzhong Lu, Ju Shen, Saverio Perugini, Jianjun Yang

Computer Science Faculty Publications

We present a tele-immersive system that enables people to interact with each other in a virtual world using body gestures in addition to verbal communication. Beyond the obvious applications, including general online conversations and gaming, we hypothesize that our proposed system would be particularly beneficial to education by offering rich visual contents and interactivity. One distinct feature is the integration of egocentric pose recognition that allows participants to use their gestures to demonstrate and manipulate virtual objects simultaneously. This functionality enables the instructor to effectively and efficiently explain and illustrate complex concepts or sophisticated problems in an intuitive manner. The …

Automatic Video Self Modeling For Voice Disorder, Ju Shen, Changpeng Ti, Anusha Raghunathan, Sen-Ching S. Cheung, Rita Patel

Computer Science Faculty Publications

Video self modeling (VSM) is a behavioral intervention technique in which a learner models a target behavior by watching a video of him- or herself. In the field of speech language pathology, the approach of VSM has been successfully used for treatment of language in children with Autism and in individuals with fluency disorder of stuttering. Technical challenges remain in creating VSM contents that depict previously unseen behaviors. In this paper, we propose a novel system that synthesizes new video sequences for VSM treatment of patients with voice disorders. Starting with a video recording of a voice-disorder patient, the proposed …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.2.1

CHANGES IN R 3.2.0

CHANGES IN R 3.1.3

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

R Foundation News, Kurt Hornik

The R Journal

Donations

New Supporting Institutions

New Supporting Members

Identifying Complex Causal Dependencies In Configurational Data With Coincidence Analysis, Michael Baumgartner, Alrik Thiem

The R Journal

We present cna, a package for performing Coincidence Analysis (CNA). CNA is a configurational comparative method for the identification of complex causal dependencies—in particular, causal chains and common cause structures—in configurational data. After a brief introduction to the method’s theoretical background and main algorithmic ideas, we demonstrate the use of the package by means of an artificial and a real-life data set. Moreover, we outline planned enhancements of the package that will further increase its applicability.

Fslr: Connecting The Fsl Software With R, John Muschelli, Elizabeth Sweeney, Martin Lindquist, Ciprian Crainiceanu

The R Journal

We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data. The fslr package performs operations on ‘nifti’ image objects in R using command-line functions from FSL, and returns R objects back to the user. fslr allows users to develop image processing and analysis pipelines based on FSL functionality while interfacing with the functionality provided by R. We present an example of the analysis of structural magnetic resonance images, which demonstrates how R users can leverage the functionality of FSL without switching …

The R Journal (June 2015) 7(1): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Peptides: A Package for Data Mining of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, and Rodrigo Torres

fanplot: An R Package for Visualising Sequential Distributions, Guy J. Abel

sparkTable: Generating Graphical Tables for Websites and Documents with R, Alexander Kowarik, Bernhard Meindl, and Matthias Templ

rdrobust: An R Package for Robust Nonparametric Inference in Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, and Rocío Titiunik

Frames2: A Package for Estimation in Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, and María del Mar Rueda

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

sae: …

R As An Environment For Reproducible Analysis Of Dna Amplification Experiments, Stefan Rödiger, Michał Burdukiewicz, Konstantin Blagodatskikh, Michael Jahn, Peter Schierack

The R Journal

There is an ever-increasing number of applications, which use quantitative PCR (qPCR) or digital PCR (dPCR) to elicit fundamentals of biological processes. Moreover, quantitative isothermal amplification (qIA) methods have become more prominent in life sciences and point-of-care diagnostics. Additionally, the analysis of melting data is essential during many experiments. Several software packages have been developed for the analysis of such datasets. In most cases, the software is either distributed as closed source software or as monolithic block with little freedom to perform highly customized analysis procedures. We argue, among others, that R is an excellent foundation for reproducible and transparent …

Sae: An R Package For Small Area Estimation, Isabel Molina, Yolanda Marhuenda

The R Journal

We describe the R package sae for small area estimation. This package can be used to obtain model-based estimates for small areas based on a variety of models at the area and unit levels, along with basic direct and indirect estimates. Mean squared errors are estimated by analytical approximations in simple models and applying bootstrap procedures in more complex models. We describe the package functions and show how to use them through examples.

Frames2: A Package For Estimation In Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, Maria Del Mar Rueda

The R Journal

Data from complex survey designs require special consideration with regard to estimation of finite population parameters and corresponding variance estimation procedures, as a consequence of significant departures from the simple random sampling assumption. In the past decade a number of statistical software packages have been developed to facilitate the analysis of complex survey data. All these statistical software packages are able to treat samples selected from one sampling frame containing all population units. Dual frame surveys are very useful when it is not possible to guarantee a complete coverage of the target population and may result in considerable cost savings …

Sparktable: Generating Graphical Tables For Websites And Documents With R, Alexander Kowarik, Bernhard Meindl, Matthias Templ

The R Journal

Visual analysis of data is important to understand the main characteristics, main trends and relationships in data sets and it can be used to assess the data quality. Using the R package sparkTable, statistical tables holding quantitative information can be enhanced by including spark-type graphs such as sparklines [] and sparkbars [].

These kind of graphics are well-known in literature and are considered as simple, intense and illustrative graphs that are small enough to fit in a single line. Thus, they can easily enrich tables and texts with additional information in a comprehensive visual way.

The R package sparkTable …

Fanplot: An R Package For Visualising Sequential Distributions, Guy J. Abel

The R Journal

Fan charts, first developed by the Bank of England in 1996, have become a standard method for visualising forecasts with uncertainty. Using shading fan charts focus the attention towards the whole distribution away from a single central measure. This article describes the basics of plotting fan charts using an R add-on package alongside some additional methods for displaying sequential distributions. Examples are based on distributions of both estimated parameters from a time series model and future values with uncertainty.

The Gridgraphics Package, Paul Murrell

The R Journal

The gridGraphics package provides a function, grid.echo(), that can be used to convert a plot drawn with the graphics package to a visually identical plot drawn using grid. This conversion provides access to a variety of grid tools for making customisations and additions to the plot that are not possible with the graphics package/

Peptides: A Package For Data Mining Of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, Rodrigo Torres

The R Journal

Antimicrobial peptides (AMP) are a promising source of antibiotics with a broad spectrum activity against bacteria and low incidence of developing resistance. The mechanism by which an AMPexecutes its function depends on a set of computable physicochemical properties from the amino acid sequence. The Peptides package was designed to allow the quick and easy computation of ten structural characteristics own of the antimicrobial peptides, with the aim of generating data to increase the accuracy in classification and design of new amino acid sequences. Moreover, the options to read and plot XVG output files from GROMACS molecular dynamics package are included.

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.