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Changes In R, R Core Team

The R Journal

CHANGES IN R 3.5.0 patched

CHANGES IN R 3.5.0

R Foundation News, Torsten Hothorn

The R Journal

Donations and members

Donations

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Conference Report: Erum 2018, Gergely Daróczi

The R Journal

The European R Users Meeting (eRum) is an international conference that aims at bringing together users of the R language living in Europe– in the years when the useR! conference is hosted outside of the continent.

The first eRum conference was held in 2016 in Poznan, Poland with around 250 attendees and 20 sessions spanning over 3 days, including more than 80 speakers. Around that time, we also held a smaller conference in Budapest: the first satRday event happened with 25 speakers and almost 200 attendees from 19 countries in 2016.

The eRum 2018 conference is heritage of these two …

Small Area Disease Risk Estimation And Visualization Using R, Paula Moraga

The R Journal

Small area disease risk estimation is essential for disease prevention and control. In this paper, we demonstrate how R can be used to obtain disease risk estimates and quantify risk factors using areal data. We explain how to define disease risk models and how to perform Bayesian inference using the INLA package. We also show how to make interactive maps of estimates using the leaflet package to better understand the disease spatial patterns and communicate the results. We show an example of lung cancer risk in Pennsylvania, United States, in year 2002, and demonstrate that R represents an excellent tool …

Cchs: An R Package For Stratified Case-Cohort Studies, Edmund Jones

The R Journal

The cchs package contains a function, also called cchs, for analyzing data from a stratified case-cohort study, as used in epidemiology. For data from this type of study, cchs calculates Estimator III of Borgan et al. (2000), which is a score-unbiased estimator for the regression coefficients in the Cox proportional hazards model. From the user’s point of view, the function is similar to coxph (in the survival package) and other widely used model-fitting functions. Convenient software has not previously been available for Estimator III since it is complicated to calculate. SAS and S-Plus code-fragments for the calculation have been published, …

Approximating The Sum Of Independent Non-Identical Binomial Random Variables, Boxiang Liu, Thomas Quertermous

The R Journal

The distribution of the sum of independent non-identical binomial random variables is frequently encountered in areas such as genomics, healthcare, and operations research. Analytical solutions for the density and distribution are usually cumbersome to find and difficult to compute. Several methods have been developed to approximate the distribution, among which is the saddlepoint approximation. However, implementation of the saddlepoint approximation is non-trivial. In this paper, we implement the saddlepoint approximation in the sinib package and provide two examples to illustrate its usage. One example uses simulated data while the other uses real-world healthcare data. The sinib package addresses the gap …

Nonparametric Independence Tests And K-Sample Tests For Large Sample Sizes Using Package Hhg, Barak Brill, Yair Heller, Ruth Heller

The R Journal

Nonparametric tests of independence and k-sample tests are ubiquitous in modern applications, but they are typically computationally expensive. We present a family of nonparametric tests that are computationally efficient and powerful for detecting any type of dependence between a pair of univariate random variables. The computational complexity of the suggested tests is sub-quadratic in sample size, allowing calculation of test statistics for millions of observations. We survey both algorithms and the HHG package in which they are implemented, with usage examples showing the implementation of the proposed tests for both the independence case and the k-sample problem. The tests are …

The R Journal (July 2018) 10(1): Complete Issue, The R Foundation

The R Journal

Editorial, John Verzani

Contributed Research Articles

A System for an Accountable Data Analysis Process in R, Jonathan Gelfond, Martin Goros, Brian Hernandez and Alex Bokov

RealVAMS: An R Package for Fitting a Multivariate Value-added Model (VAM), Jennifer Broatch, Jennifer Green, and Andrew Karl

InfoTrad: An R Package for Estimating the Probability of Informed Trading, Duygu Çelik and Murat Tiniç

RatingScaleReduction Package: Stepwise Rating Scale Item Reduction without Predictability Loss, Waldemar W. Koczkodaj, Feng Li, and Alicja Wolny-Dominiak

mmpf: Monte-Carlo Methods for Prediction Functions, Zachary M. Jones

Generalized Additive Model Multiple Imputation by Chained Equations with Package ImputeRobust, Daniel Salfran and …

Grpstring: An R Package For Analysis Of Groups Of Strings, Hui Tang, Elizabeth L. Day, Molly B. Atkinson, Norbert J. Pienta

The R Journal

The R package GrpString was developed as a comprehensive toolkit for quantitatively analyzing and comparing groups of strings. It offers functions for researchers and data analysts to prepare strings from event sequences, extract common patterns from strings, and compare patterns be tween string vectors. The package also finds transition matrices and complexity of strings, determines clusters in a string vector, and examines the statistical difference between two groups of strings.

Lba: An R Package For Latent Budget Analysis, Enio G. Jelihovschi, Ivan Bezerra Allaman

The R Journal

The latent budget model is a mixture model for compositional data sets in which the entries, a contingency table, may be either realizations from a product multinomial distribution or distribution free. Based on this model, the latent budget analysis considers the interactions of two variables; the explanatory (row) and the response (column) variables. The package lba uses expectation-maximization and active constraints method (ACM) to carry out, respectively, the maximum likelihood and the least squares estimation of the model parameters. It contains three main functions, lba which performs the analysis, goodnessfit for model selection and goodness of fit and the plotting …

Tackling Uncertainties Of Species Distribution Model Projections With Package Mopa, M. Iturbide, J. Bedia, J.M. Gutiérrez

The R Journal

Species Distribution Models (SDMs) constitute an important tool to assist decision-making in environmental conservation and planning in the context of climate change. Nevertheless, SDM projections are affected by a wide range of uncertainty factors (related to training data, climate projections and SDM techniques), which limit their potential value and credibility. The new package mopa provides tools for designing comprehensive multi-factor SDM ensemble experiments, combining multiple sources of uncertainty (e.g. baseline climate, pseudo-absence realizations, SDM techniques, future projections) and allowing to assess their contribution to the overall spread of the ensemble projection. In addition, mopa is seamlessly integrated with the climate4R …

Panjen: An R Package For Ranking Transformations In A Linear Regression, Cathrine Ulla Jensen, Toke Emil Panduro

The R Journal

PanJen is an R-package for ranking transformations in linear regressions. It provides users with the ability to explore the relationship between a dependent variable and its independent variables. The package offers an easy and data-driven way to choose a functional form in multiple linear regression models by comparing a range of parametric transformations. The parametric functional forms are benchmarked against each other and a non-parametric transformation. The package allows users to generate plots that show the relation between a covariate and the dependent variable. Furthermore, PanJen will enable users to specify specific functional transformations, driven by a priori and theory-based …

Mmpf: Monte-Carlo Methods For Prediction Functions, Zachary M. Jones

The R Journal

Machine learning methods can often learn high-dimensional functions which generalize well but are not human interpretable. The mmpf package marginalizes prediction functions using Monte-Carlo methods, allowing users to investigate the behavior of these learned functions, as on a lower dimensional subset of input features: partial dependence and variations thereof. This makes machine learning methods more useful in situations where accurate prediction is not the only goal, such as in the social sciences where linear models are commonly used because of their interpretability.

Many methods for estimating prediction functions produce estimated functions which are not directly human-interpretable because of their complexity: …

Infotrad: An R Package For Estimating The Probability Of Informed Trading, Duygu Çelik, Murat Tiniç

The R Journal

The purpose of this paper is to introduce the R package InfoTrad for estimating the probability of informed trading (PIN) initially proposed by Easley et al. (1996). PIN is a popular information asymmetry measure that proxies the proportion of informed traders in the market. This study provides a short survey on alternative estimation techniques for the PIN. There are many problems documented in the existing literature in estimating PIN. InfoTrad package aims to address two problems. First, the sequential trading structure proposed by Easley et al. (1996) and later extended by Easley et al. (2002) is prone to sample selection …

Static Analysis Of Context Leaks In Android Applications, Flavio Toffalini, Jun Sun, Martín Cohoa

Research Collection School Of Computing and Information Systems

Android native applications, written in Java and distributed in APK format, are widely used in mobile devices. Their specific pattern of use lets the operating system control the creation and destruction of key resources, such as activities and services (contexts). Programmers are not supposed to interfere with such lifecycle events. Otherwise contexts might be leaked, i.e. they will never be deallocated from memory, or be deallocated too late, leading to memory exhaustion and frozen applications. In practice, it is easy to write incorrect code, which hinders garbage collection of contexts and subsequently leads to context leakage.In this work, we present …

Overfitting In Automated Program Repair: Challenges And Solutions, Dinh Xuan Bach Le

Dissertations and Theses Collection (Open Access)

This chapter discusses the main problem and motivation of this dissertation. It also discusses a quantification of various research issues directly related to the dissertation. A summary of works done will also be presented along with the structure of the dissertation.

Funqual: User-Defined, Statically-Checked Call Graph Constraints In C++, Andrew P. Nelson

Master's Theses

Static analysis tools can aid programmers by reporting potential programming mistakes prior to the execution of a program. Funqual is a static analysis tool that reads C++17 code ``in the wild'' and checks that the function call graph follows a set of rules which can be defined by the user. This sort of analysis can help the programmer to avoid errors such as accidentally calling blocking functions in time-sensitive contexts or accidentally allocating memory in heap-sensitive environments. To accomplish this, we create a type system whereby functions can be given user-defined type qualifiers and where users can define their own …

Compiler Optimization Effects On Register Collisions, Jonathan S. Tan

Master's Theses

We often want a compiler to generate executable code that runs as fast as possible. One consideration toward this goal is to keep values in fast registers to limit the number of slower memory accesses that occur. When there are not enough physical registers available for use, values are ``spilled'' to the runtime stack. The need for spills is discovered during register allocation wherein values in use are mapped to physical registers. One factor in the efficacy of register allocation is the number of values in use at one time (register collisions). Register collision is affected by compiler optimizations that …

An Empirical Study Of Alias Analysis Techniques, Andrew T. Tran

Master's Theses

As software projects become larger and more complex, software optimization at that scale is only feasible through automated means. One such component of software optimization is alias analysis, which attempts to determine which variables in a program refer to the same area in memory, and is used to relocate instructions to improve performance without interfering with program execution. Several alias analyses have been proposed over the past few decades, with varying degrees of precision and time and space complexity, but few studies have been conducted to compare these techniques with one another, nor to measure with program data to confirm …

Poster: Towards Safe Refactoring For Intelligent Parallelization Of Java 8 Streams, Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

The Java 8 Stream API sets forth a promising new programming model that incorporates functional-like, MapReduce-style features into a mainstream programming language. However, using streams correctly and efficiently may involve subtle considerations. In this poster, we present our ongoing work and preliminary results towards an automated refactoring approach that assists developers in writing optimal stream code. The approach, based on ordering and typestate analysis, determines when it is safe and advantageous to convert streams to parallel and optimize a parallel streams.