Numerical Analysis and Scientific Computing Commons^™

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor 3.14 was released on 27 October, 2021. It is compatible with R 4.1.0 and consists of 2083 software packages, 408 experiment data packages, 904 up-to-date annotation packages, and 29 workflows.

Changes In R, Tomas Kalibera, Sebastian Meyer, Kurt Hornik, Gennadiy Starostin, Luke Tierney

The R Journal

We present important changes in the development version of R (referred to as R-devel, to become R 4.2) and give a summary of the new search engine interfaced by RSiteSearch(). Some statistics on bug tracking activities in 2021 are also provided.

Rpese: Risk And Performance Estimators Standard Errors With Serially Dependent Data, Anthony-Alexander Christidis, R Douglas Martin

The R Journal

The R package RPESE (Risk and Performance Estimators Standard Errors) implements a new method for computing accurate standard errors of risk and performance estimators when returns are serially dependent. The new method makes use of the representation of a risk or performance estimator as a summation of a time series of influence-function (IF) transformed returns, and computes estimator standard errors using a sophisticated method of estimating the spectral density at frequency zero of the time series of IF-transformed returns. Two additional packages used by RPESE are introduced, namely RPEIF which computes and provides graphical displays of the IF of risk …

The Vote Package: Single Transferable Vote And Other Electoral Systems In R, Adrian E. Raftery, Hana ŠevčÍková, Bernard W. Silverman

The R Journal

We describe the vote package in R, which implements the plurality (or first-past-the-post), two-round runoff, score, approval, and Single Transferable Vote (STV) electoral systems, as well as methods for selecting the Condorcet winner and loser. We emphasize the STV system, which we have found to work well in practice for multi-winner elections with small electorates, such as committee and council elections, and the selection of multiple job candidates. For single-winner elections, STV is also called Instant Runoff Voting (IRV), Ranked Choice Voting (RCV), or the alternative vote (AV) system. The package also implements the STV system with equal preferences, for …

Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language

Bssm: Bayesian Inference Of Non-Linear And Non-Gaussian State Space Models In R, Jouni Helske, Matti Vihola

The R Journal

We present an R package bssm for Bayesian non-linear/non-Gaussian state space modeling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package also accommodates discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package also implements a direct pseudo-marginal MCMC and a delayed acceptance pseudo-marginal MCMC using intermediate approximations. The package offers an easy-to-use interface to define models with linear-Gaussian state …

Openskies - Integration Of Aviation Data Into The R Ecosystem, Rafael Ayala, Daniel Ayala, Lara Sellés Vidal, David Ruiz

The R Journal

Aviation data has become increasingly more accessible to the public thanks to the adoption of technologies such as Automatic Dependent Surveillance-Broadcast (ADS-B) and Mode S, which provide aircraft information over publicly accessible radio channels. Furthermore, the OpenSky Network provides multiple public resources to access such air traffic data from a large network of ADS-B receivers. Here, we present openSkies, the first R package for processing public air traffic data. The package provides an interface to the OpenSky Network resources, standardized data structures to represent the different entities involved in air traffic data, and functionalities to analyze and visualize such …

Passed: Calculate Power And Sample Size For Two Sample Tests, Jinpu Li, Ryan .. Knigge, Kaiyi Chen, Emily V. Leary

The R Journal

Power and sample size estimation are critical aspects of study design to demonstrate minimized risk for subjects and justify the allocation of time, money, and other resources. Researchers often work with response variables that take the form of various distributions. Here, we present an R package, PASSED, that allows flexibility with seven common distributions and multiple options to accommodate sample size or power analysis. The relevant statistical theory, calculations, and examples for each distribution using PASSED are discussed in this paper.

Automatic Time Series Forecasting With Ata Method In R: Ataforecasting Package, Ali Sabri Taylan, Güçkan Yapar, Hanife Taylan Selamlar

The R Journal

Ata method is a new univariate time series forecasting method that provides innovative solutions to issues faced during the initialization and optimization stages of existing methods. The Ata method’s forecasting performance is superior to existing methods in terms of easy implementation and accurate forecasting. It can be applied to non-seasonal or deseasonalized time series, where the deseasonalization can be performed via any preferred decomposition method. The R package ATAforecasting was developed as a comprehensive toolkit for automatic time series forecasting. It focuses on modeling all types of time series components with any preferred Ata methods and handling seasonality patterns by …

A New Versatile Discrete Distribution, Rolf Turner

The R Journal

This paper introduces a new flexible distribution for discrete data. Approximate moment estimators of the parameters of the distribution, to be used as starting values for numerical optimization procedures, are discussed. “Exact” moment estimation, effected via a numerical procedure, and maximum likelihood estimation, are considered. The quality of the results produced by these estimators is assessed via simulation experiments. Several examples are given of fitting instances of the new distribution to real and simulated data. It is noted that the new distribution is a member of the exponential family. Expressions for the gradient and Hessian of the log-likelihood of the …

Robustbf: An R Package For Robust Solution To The Behrens-Fisher Problem, Gamze Güven, ŞÜkrü Acıtaş, Hatice ŞAmkar, Birdal ŞEnoğLu

The R Journal

Welch’s two-sample t-test based on least squares (LS) estimators is generally used to test the equality of two normal means when the variances are not equal. However, this test loses its power when the underlying distribution is not normal. In this paper, two different tests are proposed to test the equality of two long-tailed symmetric (LTS) means under heterogeneous variances. Adaptive modified maximum likelihood (AMML) estimators are used in developing the proposed tests since they are highly efficient under LTS distribution. An R package called RobustBF is given to show the implementation of these tests. Simulated Type I error rates …

Volesti: Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language.

Passed: Calculate Power And Sample Size For Two Sample Tests, University Of Missouri Li, Ryan P. Knigge, Kaiyi Chen, Emily V. Leary

The R Journal

Power and sample size estimation are critical aspects of study design to demonstrate minimized risk for subjects and justify the allocation of time, money, and other resources. Researchers often work with response variables that take the form of various distributions. Here, we present an R package, PASSED, that allows flexibility with seven common distributions and multiple options to accommodate sample size or power analysis. The relevant statistical theory, calculations, and examples for each distribution using PASSED are discussed in this paper.

Robust And Efficient Optimization Using A Marquardt-Levenberg Algorithm With R Package Marqlevalg, Viviane Philipps, Boris P. Hejblum, Mélanie Prague, Daniel Commenges, Cécile Proust-Lima

The R Journal

Implementations in R of classical general-purpose algorithms for local optimization generally have two major limitations which cause difficulties in applications to complex problems: too loose convergence criteria and too long calculation time. By relying on a Marquardt-Levenberg algorithm (MLA), a Newton-like method particularly robust for solving local optimization problems, we provide with marqLevAlg package an efficient and general-purpose local optimizer which (i) prevents convergence to saddle points by using a stringent convergence criterion based on the relative distance to minimum/maximum in addition to the stability of the parameters and of the objective function; and (ii) reduces the computation time in …

Emss: New Em-Type Algorithms For The Heckman Selection Model In R, Kexuan Yang, Sang Kyu Lee, Jun Zhao, Hyoung-Moon Kim

The R Journal

When investigators observe non-random samples from populations, sample selectivity problems may occur. The Heckman selection model is widely used to deal with selectivity problems. Based on the EM algorithm, Zhao et al. (2020) developed three algorithms, namely, ECM, ECM(NR), and ECME(NR), which also have the EM algorithm’s main advantages: stability and ease of implementation. This paper provides the implementation of these three new EM-type algorithms in the package EMSS and illustrates the usage of the package on several simulated and real data examples. The comparison between the maximum likelihood estimation method (MLE) and three new EM-type algorithms in robustness issues …

Bayessenmc: An R Package For Bayesian Sensitivity Analysis Of Misclassification, Jinhui Yang, Lifeng Lin, Haitao Chu

The R Journal

In case–control studies, the odds ratio is commonly used to summarize the association between a binary exposure and a dichotomous outcome. However, exposure misclassification frequently appears in case–control studies due to inaccurate data reporting, which can produce bias in measures of association. In this article, we implement a Bayesian sensitivity analysis of misclassification to provide a full posterior inference on the corrected odds ratio under both non-differential and differential misclassification. We present an R (R Core Team, 2018) package BayesSenMC, which provides user-friendly functions for its implementation. The usage is illustrated by a real data analysis on the association between …

Dad: An R Package For Visualisation, Classification And Discrimination Of Multivariate Groups Modelled By Their Densities, Rachid Boumaza, Pierre Santagostini, Smail Yousfi, Sabine Demotes-Mainard

The R Journal

Multidimensional scaling (MDS), hierarchical cluster analysis (HCA), and discriminant analysis (DA) are classical techniques which deal with data made of n individuals and p variables. When the individuals are divided into T groups, the R package dad associates with each group a multivariate probability density function and then carries out these techniques on the densities, which are estimated by the data under consideration. These techniques are based on distance measures between densities: chi-square, Hellinger, Jeffreys, Jensen-Shannon, and L^p for discrete densities, Hellinger , Jeffreys, L² , and 2-Wasserstein for Gaussian densities, and L² for numeric non-Gaussian densities …

Stratigrapher: Concepts For Litholog Generation In R, Sébastien Wouters, Anne-Christine Da Silva, Frédéric Boulvain, Xavier Devleeschouwer

The R Journal

The StratigrapheR package proposes new concepts for the generation of lithological logs, or lithologs, in R. The generation of lithologs in a scripting environment opens new opportunities for the processing and analysis of stratified geological data. Among the new concepts presented: new plotting and data processing methodologies, new general R functions, and computer-oriented data conventions are provided. The package structure allows for these new concepts to be further improved, which can be done independently by any R user. The current limitations of the package are highlighted, along with the limitations in R for geological data processing, to help identify the …

Msae: An R Package Of Multivariate Fay-Herriot Models For Small Area Estimation, Novia Permatasari, Azka Ubaidillah

The R Journal

The paper introduces an R Package of multivariate Fay-Herriot models for small area estimation named msae. This package implements four types of Fay-Herriot models, including univariate Fay-Herriot model (model 0), multivariate Fay-Herriot model (model 1), autoregressive multivariate Fay-Herriot model (model 2), and heteroskedastic autoregressive multivariate Fay-Herriot model (model 3). It also contains some datasets generated based on multivariate Fay-Herriot models. We describe and implement functions through various practical examples. Multivariate Fay-Herriot models produce a more efficient parameter estimation than direct estimation and univariate model.

Estimating Social Influence Effects In Networks Using A Latent Space Adjusted Approach In R, Ran Xu

The R Journal

Social influence effects have been extensively studied in various empirical network research. However, many challenges remain in estimating social influence effects in networks, as influence effects are often entangled with other factors, such as homophily in the selection process and the common social-environmental factors that individuals are embedded in. Methods currently available either do not solve these problems or require stringent assumptions. Recent works by Xu (2018) and others have shown that a latent space adjusted approach based on the latent space model has the potential to disentangle the influence effects from other processes, and the simulation evidence has shown …

G2f As A Novel Tool To Find And Fill Gaps In Metabolic Networks, Daniel Osorio, Kelly Botero, Andrés Pinzón Velasco, Nicolás Mendoza-Mejía, Felipe Rojas-Rodríguez, George Barreto, Janneth González

The R Journal

During the building of a genome-scale metabolic model, there are several dead-end metabolites and substrates which cannot be imported, produced, nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from …

Rejoinder: Software Engineering And R Programming, Melina Vidoni

The R Journal

It is a pleasure to take part in such fruitful discussion about the relationship between Software Engineering and R programming, and what could be gain by allowing each to look more closely at the other. Several discussants make valuable arguments that ought to be further discussed

The R Quest: From Users To Developers, Simon Urbanek

The R Journal

R is not a programming language, and this produces the inherent dichotomy between analytics and software engineering. With the emergence of data science, the opportunity exists to bridge this gap, especially through teaching practices.

Software Engineering And R Programming: A Call For Research, Melina Vidoni

The R Journal

Although R programming has been a part of research since its origins in the 1990s, few studies address scientific software development from a Software Engineering (SE) perspective. The past few years have seen unparalleled growth in the R community, and it is time to push the boundaries of SE research and R programming forwards. This paper discusses relevant studies that close this gap Additionally, it proposes a set of good practices derived from those findings aiming to act as a call-to-arms for both the R and RSE (Research SE) community to explore specific, interdisciplinary paths of research

Editorial, Dianne Cook

The R Journal

On behalf of the R Foundation and the Editorial board, I am pleased to present Volume 13 Issue 2 of the R Journal. This is the biggest issue ever!

First, some news from the Editorial board. A big thank you to Mike Kane, who has finished his term. As Editor-in-Chief in 2020, Mike expanded operations to include Associate Editors in the reviewing process. The R Journal now has a team of 20 Associate Editors. This has helped to manage the increasing number of submissions. We welcome new Associate Editors, Przemek Biecek, Chris Brunsdon, Mine Çetinkaya-Rundel, Kieran Healy, Adam Loy, Priyanga …

Elliptical Symmetry Tests In R, Slad̄Ana Babić, Christophe Ley, Marko Palangetić

The R Journal

The assumption of elliptical symmetry has an important role in many theoretical developments and applications. Hence, it is of primary importance to be able to test whether that assumption actually holds true or not. Various tests have been proposed in the literature for this problem. To the best of our knowledge, none of them has been implemented in R. This article describes the R package ellipticalsymmetry which implements several well-known tests for elliptical symmetry together with some recent tests. We demonstrate the testing procedures with a real data example.

An R Package For Robust Solution To The Behrens-Fisher Problem, Gamze Güven, ŞÜkrü Acıtaş, Hatice ŞAmkar, Birdal ŞEnoğLu

The R Journal

Welch’s two-sample t-test based on least squares (LS) estimators is generally used to test the equality of two normal means when the variances are not equal. However, this test loses its power when the underlying distribution is not normal. In this paper, two different tests are proposed to test the equality of two long-tailed symmetric (LTS) means under heterogeneous variances. Adaptive modified maximum likelihood (AMML) estimators are used in developing the proposed tests since they are highly efficient under LTS distribution. An R package called RobustBF is given to show the implementation of these tests. Simulated Type I error rates …

Diproperm: An R Package For The Diproperm Test, Andrew G. Allmon, J.S. Marron, Michael G. Hudgens

The R Journal

High-dimensional low sample size (HDLSS) data sets frequently emerge in many biomedical applications. The direction-projection-permutation (DiProPerm) test is a two-sample hypothesis test for comparing two high-dimensional distributions. The DiProPerm test is exact, i.e., the type I error is guaranteed to be controlled at the nominal level for any sample size, and thus is applicable in the HDLSS setting. This paper discusses the key components of the DiProPerm test, introduces the diproperm R package, and demonstrates the package on a real-world data set

Tramme: Mixed-Effects Transformation Models Using Template Model Builder, Bálint Tamási, Torsten Hothorn

The R Journal

Linear transformation models constitute a general family of parametric regression models for discrete and continuous responses. To accommodate correlated responses, the model is extended by incorporating mixed effects. This article presents the R package tramME, which builds on existing implementations of transformation models (mlt and tram packages) as well as Laplace approximation and automatic differentiation (using the TMB package), to calculate estimates and perform likelihood inference in mixed-effects transformation models. The resulting framework can be readily applied to a wide range of regression problems with grouped data structures.

Changes On Cran, Kurt Hornik, Uwe Ligges, Achim Zeileis

The R Journal

In the past 6 months, 1077 new packages were added to the CRAN package repository. 113 packages were unarchived and 331 were archived. The following shows the growth of the number of active packages in the CRAN package repository: