Programming Languages and Compilers Commons^™

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 …

Zoib: An R Package For Bayesian Inference For Beta Regression And Zero/One Inflated Beta Regression, Fang Liu, Yunchuan Kong

The R Journal

The beta distribution is a versatile function that accommodates a broad range of probability distribution shapes. Beta regression based on the beta distribution can be used to model a response variable y that takes values in open unit interval (0,1). Zero/one inflated beta (ZOIB) regression models can be applied when y takes values from closed unit interval [0,1]. The ZOIB model is based a piecewise distribution that accounts for the probability mass at 0 and 1, in addition to the probability density within (0,1). This paper introduces an R package– zoib that provides Bayesian inferences for a class of ZOIB …

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. …

The R Journal (December 2015) 7(2): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Fitting Conditional and Simultaneous Autoregressive Spatial Models in hglm, Moudud Alam, Lars Rönnegård, and Xia Shen

VSURF: An R Package for Variable Selection Using Random Forests, Robin Genuer, Jean-Michel Poggi, and Christine Tuleau-Malot

zoib: An R Package for Bayesian Inference for Beta Regression and Zero/One Inflated Beta Regression, Fang Liu, and Yunchuan Kong

apc: An R Package for Age-Period-Cohort Analysis, Bent Nielsen

QuantifQuantile: An R Package for Performing Quantile Regression Through Optimal Quantization, Isabelle Charlier, Davy Paindaveine, and Jérôme Saracco

Numerical Evaluation of the Gauss Hypergeometric Function with the hypergeo Package, Robin K. S. …

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 …

Practools: Computations For Design Of Finite Population Samples, Richard Valliant, Jill A. Dever, Frauke Kreuter

The R Journal

PracTools is an R package with functions that compute sample sizes for various types of finite population sampling designs when totals or means are estimated. One-, two-, and three-stage designs are covered as well as allocations for stratified sampling and probability proportional to size sampling. Sample allocations can be computed that minimize the variance of an estimator subject to a budget constraint or that minimize cost subject to a precision constraint. The package also contains some specialized functions for estimating variance components and design effects. Several finite populations are included that are useful for classroom instruction.

An R Package For The Panel Approach Method For Program Evaluation: Pampe, Ainhoa Vega-Bayo

The R Journal

The pampe package for R implements the panel data approach method for program evaluation designed to estimate the causal effects of political interventions or treatments. This procedure exploits the dependence among cross-sectional units to construct a counterfactual of the treated unit(s), and it is an appropriate method for research events that occur at an aggregate level like countries or regions and that affect only one or a small number of units. The implementation of the pampe package is illustrated using data from Hong Kong and 24 other units, by examining the economic impact of the political and economic integration of …

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). …

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.

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.

Changes In R, The R Core Team

The R Journal

CHANGES IN R 3.2.3

CHANGES IN R 3.2.2

Open-Channel Computation With R, Michael C. Koohafkan, Bassam A. Younis

The R Journal

The rivr package provides a computational toolset for simulating steady and unsteady one dimensional flows in open channels. It is designed primarily for use by instructors of undergraduate and graduate-level open-channel hydrodynamics courses in such diverse fields as river engineering, physical geography and geophysics. The governing equations used to describe open-channel flows are briefly presented, followed by example applications. These include the computation of gradually varied flows and two examples of unsteady flows in channels—namely, the tracking of the evolution of a flood wave in a channel and the prediction of extreme variation in the water-surface profile that results when …

Mmpp: A Package For Calculating Similarity And Distance Metrics For Simple And Marked Temporal Point Processes, Hideitsu Hino, Ken Takano, Noboru Murata

The R Journal

A simple temporal point process (SPP) is an important class of time series, where the sample realization of the process is solely composed of the times at which events occur. Particular examples of point process data are neuronal spike patterns or spike trains, and a large number of distance and similarity metrics for those data have been proposed. A marked point process (MPP) is an extension of a simple temporal point process, in which a certain vector valued mark is associated with each of the temporal points in the SPP. Analyses of MPPs are of practical importance because instances of …

Mtk: A General-Purpose And Extensible R Environment For Uncertainty And Sensitivity Analyses Of Numerical Experiments, Juhui Wang, Robert Faivre, Hervé Richard, Hervé Monod

The R Journal

Along with increased complexity of the models used for scientific activities and engineering come diverse and greater uncertainties. Today, effectively quantifying the uncertainties contained in a model appears to be more important than ever. Scientific fellows know how serious it is to calibrate their model in a robust way, and decision-makers describe how critical it is to keep the best effort to reduce the uncertainties about the model. Effectively accessing the uncertainties about the model requires mastering all the tasks involved in the numerical experiments, from optimizing the experimental design to managing the very time consuming aspect of model simulation …

Vsurf: An R Package For Variable Selection Using Random Forests, Robin Genuer, Jean-Michel Poggi, Christine Tuleau-Malot

The R Journal

This paper describes the R package VSURF. Based on random forests, and for both regression and classification problems, it returns two subsets of variables. The first is a subset of important variables including some redundancy which can be relevant for interpretation, and the second one is a smaller subset corresponding to a model trying to avoid redundancy focusing more closely on the prediction objective. The two-stage strategy is based on a preliminary ranking of the explanatory variables using the random forests permutation-based score of importance and proceeds using a stepwise forward strategy for variable introduction. The two proposals can …

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.

Srcs: Statistical Ranking Color Scheme For Visualizing Parameterized Multiple Pairwise Comparisons With R, Pablo J. Villacorta, José A. Sáez

The R Journal

The problem of comparing a new solution method against existing ones to find statistically significant differences arises very often in sciences and engineering. When the problem instance being solved is defined by several parameters, assessing a number of methods with respect to many problem configurations simultaneously becomes a hard task. Some visualization technique is required for presenting a large number of statistical significance results in an easily interpretable way. Here we review an existing color-based approach called Statistical Ranking Color Scheme (SRCS) for displaying the results of multiple pairwise statistical comparisons between several methods assessed separately on a number of …

Toward Unification Of Explicit And Implicit Invocation-Style Programming, Yoonsik Cheon

Departmental Technical Reports (CS)

Subprograms like procedures and methods can be invoked explicitly or implicitly; in implicit invocation, an event implicitly causes the invocation of subprograms that are registered an interest in the event. Mixing these two styles is common in programming and often unavoidable in developing such software as GUI applications and event-based control systems. However, it isn't also uncommon for the mixed use to complicate programming logic and thus produce unclean code, code that is hard to read and understand. We show, through a small but realistic example, that the problem is not much on mixing two different styles itself but more …

A Systematic Derivation Of Loop Specifications Using Patterns, Aditi Barua, Yoonsik Cheon

Departmental Technical Reports (CS)

Any non-trivial program contains loop control structures such as while, for and do statements. A formal correctness proof of code containing loop control structures is typically performed using an induction-based technique, and oftentimes the most challenging step of an inductive proof is formulating a correct induction hypothesis. An incorrectly-formulated induction hypothesis will surely lead to a failure of the proof. In this paper we propose a systematic approach for formulating and driving specifications of loop control structures for formal analysis and verification of programs. We explain our approach using while loops and a functional program verification technique in which a …

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.