Programming Languages and Compilers Commons^™

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.

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.

A Cultural Diffusion Model For The Rise And Fall Of Programming Languages, Sergi Valverde, Ricard V. Solé

Human Biology Open Access Pre-Prints

Our interaction with complex computing machines is mediated by programming languages (PLs) which constitute one of the major innovations in the evolution of technology. PLs allowed a flexible, scalable and fast use of hardware and are largely responsible for shaping the history of information technology since the rise of computers in the 1950s. The rapid growth and impact of computers was followed closely by the development of programming languages. As it occurs with natural, human languages, they emerged and got extinct. There has been always a diversity of coexisting PLs that somewhat compete among them, while occupying special niches. Here …

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.

Verifying Parameterized Timed Security Protocols, Li Li, Jun Sun, Yang Liu, Jin Song Dong

Research Collection School Of Computing and Information Systems

Quantitative timing is often explicitly used in systems for better security, e.g., the credentials for automatic website logon often has limited lifetime. Verifying timing relevant security protocols in these systems is very challenging as timing adds another dimension of complexity compared with the untimed protocol verification. In our previous work, we proposed an approach to check the correctness of the timed authentication in security protocols with fixed timing constraints. However, a more difficult question persists, i.e., given a particular protocol design, whether the protocol has security flaws in its design or it can be configured secure with proper parameter values? …

Introducing Faceted Exception Handling For Dynamic Information Flow, Sri Tej Narala

Master's Projects

JavaScript is most commonly used as a part of web browsers, especially client- side scripts interacting with the user. JavaScript is also the source of many security problems, which includes cross-site scripting attacks. The primary challenge is that code from untrusted sources run with full privileges on the client side, thus lead- ing to security breaches. This paper develops information flow controls with proper exception handling to prevent violations of data confidentiality and integrity.

Faceted values are a mechanism to handle dynamic information flow security in a way that overcomes the limitations caused by dynamic execution, but previous work has …

Adding Syntax Parameters To The Sweet.Js Macro Library For Javascript, Vimal Kumar

Master's Projects

Lisp and Scheme have demonstrated the power of macros to enable programmers to evolve and craft languages. A macro is a rule or pattern that specifies how a certain input sequence should be mapped to an output sequence according to some defined procedure. Using a macro system a programmer can introduce new syntactic elements to the programming language. Macros found in a program are expanded by a macro expander and allow a programmer to enable code reuse. Mozilla Sweet.JS provides a way for developers to enrich their JavaScript code by adding new syntax to the language through the use of …

Operational Semantics For Featherweight Lua, Hanshu Lin

Master's Projects

Lua is a small, embedded language to provide scripting in other languages. De- spite a clean, minimal syntax, it is still too complex for formal reasoning because of some syntactic sugar or specific syntax structures in Lua.

This thesis develops Featherweight Lua (FWLua), following the tradition of lan- guages like Featherweight Java[1] and Featherweight JavaScript[2]. The goal is to develop a core of language features that, while remaining simple enough for formal reasoning, also remain faithful to the central characteristics of the language. Specifi- cally for Lua, the core features that are essential for our modeling include:

∙ First-class functions …

Heuristic Collective Learning For Efficient And Robust Emergence Of Social Norms, Jianye Hao, Jun Sun, Dongping Huang, Yi Cai, Chao Yu

Research Collection School Of Computing and Information Systems

In multiagent systems, social norms is a useful technique in regulating agents’ behaviors to achieve coordination or cooperation among agents. One important research question is to investigate how a desirable social norm can be evolved in a bottom-up manner through local interactions. In this paper, we propose two novel learning strategies under the collective learning framework: collective learning EV-l and collective learning EV-g, to efficiently facilitate the emergence of social norms. Experimental results show that both learning strategies can support the emergence of desirable social norms more efficiently in a much broader range of multiagent interaction scenarios than previous work, …