Volume 13/2

Articles published in the December 2021 issue

Complete issue

Table of contents

Dianne Cook 4

Discussion Article

Software Engineering and R Programming: A Call for Research
Melina Vidoni 6

We Need Trustworthy R Packages
William Michael Landau 15

The R Developer Community Does Have a Strong Software Engineering Culture
Maëlle Salmon and Karthik Ram 18

The R Quest: from Users to Developers
Simon Urbanek 22

Rejoinder: Software Engineering and R Programming
Melina Vidoni 25

Contributed Research Articles

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 and Janneth González 28

lg: An R package for Local Gaussian Approximations
Håkon Otneim 38

Estimating Social Influence Effects in Networks Using A Latent Space Adjusted Approach in R
Ran Xu 57

survidm: An R package for Inference and Prediction in an Illness-Death Model
Gustavo Soutinho, Marta Sestelo and Luís Meira-Machado 70

Multiple Imputation and Synthetic Data Generation with NPBayesImputeCat
Jingchen Hu, Olanrewaju Akande and Quanli Wang 90

msae: An R Package of Multivariate Fay-Herriot Models for Small Area Estimation
Novia Permatasari and Azka Ubaidillah 111

cat.dt: An R package for fast construction of accurate Computerized Adaptive Tests using Decision Trees
Javier Rodríguez-Cuadrado, Juan C. Laria and David Delgado-Gómez 123

A GUIded tour of Bayesian regression
Andrés Ramírez–Hassan and Mateo Graciano-Londoño 135

StratigrapheR: Concepts for Litholog Generation in R
Sébastien Wouters, Anne-Christine Da Silva, Frédéric Boulvain and Xavier Devleeschouwer 153

dad: an R Package for Visualisation, Classification and Discrimination of Multivariate Groups Modelled by their Densities
Rachid Boumaza, Pierre Santagostini, Smail Yousfi and Sabine Demotes-Mainard 179

NGSSEML: Non-Gaussian State Space with Exact Marginal Likelihood
Thiago R. Santos, Glaura C. Franco and Dani Gamerman 208

BayesSenMC: an R package for Bayesian Sensitivity Analysis of Misclassification
Jinhui Yang, Lifeng Lin and Haitao Chu 228

PAsso: an R Package for Assessing Partial Association between Ordinal Variables
Shaobo Li, Xiaorui Zhu, Yuejie Chen and Dungang Liu 239

bcmixed: A Package for Median Inference on Longitudinal Data with the Box–Cox Transformation
Kazushi Maruo, Ryota Ishii, Yusuke Yamaguchi and Masahiko Gosho 253

diproperm: An R Package for the DiProPerm Test
Andrew G. Allmon, J.S. Marron and Michael G. Hudgens 266

A Unifying Framework for Parallel and Distributed Processing in R using Futures
Henrik Bengtsson 273

MatchThem:: Matching and Weighting after Multiple Imputation
Farhad Pishgar, Noah Greifer, Clémence Leyrat and Elizabeth Stuart 292

EMSS: New EM-type algorithms for the Heckman selection model in R
Kexuan Yang, Sang Kyu Lee, Jun Zhao and Hyoung-Moon Kim 306

Analysis of Corneal Data in R with the rPACI Package
Darío Ramos-López and Ana D. Maldonado 321

MAINT.Data: Modelling and Analysing Interval Data in R
A. Pedro Duarte Silva, Paula Brito, Peter Filzmoser and José G. Dias 336

Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package marqLevAlg
Viviane Philipps, Boris P. Hejblum, Mélanie Prague, Daniel Commenges and Cécile Proust-Lima 365

DRHotNet: An R package for detecting differential risk hotspots on a linear network
Álvaro Briz-Redón, Francisco Martínez-Ruiz and Francisco Montes 380

tramME: Mixed-Effects Transformation Models Using Template Model Builder
Bálint Tamási and Torsten Hothorn 398

miRecSurv Package: Prentice-Williams-Peterson Models with Multiple Imputation of Unknown Number of Previous Episodes
David Moriña, Gilma Hernández-Herrera and Albert Navarro 419

An R package for Non-Normal Multivariate Distributions: Simulation and Probability Calculations from Multivariate Lomax (Pareto Type II) and Other Related Distributions
Zhixin Lun and Ravindra Khattree 427

CompModels: A Suite of Computer Model Test Functions for Bayesian Optimization
Tony Pourmohamad 441

spfilteR: An R package for Semiparametric Spatial Filtering with Eigenvectors in (Generalized) Linear Models
Sebastian Juhl 450

SIQR: An R Package for Single-index Quantile Regression
Tianhai Zu and Yan Yu 460

mgee2: An R package for marginal analysis of longitudinal ordinal data with misclassified responses and covariates
Yuliang Xu, Shuo Shuo Liu and Grace Y. Yi 471

A New Versatile Discrete Distribution
Rolf Turner 485

Automatic Time Series Forecasting with Ata Method in R: ATAforecasting Package
Ali Sabri Taylan, Güçkan Yapar and Hanife Taylan Selamlar 507

PASSED: Calculate Power and Sample Size for Two Sample Tests
Jinpu Li, Ryan P. Knigge, Kaiyi Chen and Emily V. Leary 542

spNetwork: A Package for Network Kernel Density Estimation
Jeremy Gelb 561

bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R
Jouni Helske and Matti Vihola 578

openSkies - Integration of Aviation Data into the R Ecosystem
Rafael Ayala, Daniel Ayala, Lara Sellés Vidal and David Ruiz 590

Generalized Linear Randomized Response Modeling using GLMMRR
Jean-Paul Fox, Konrad Klotzke and Duco Veen 600

Visual Diagnostics for Constrained Optimisation with Application to Guided Tours
H. Sherry Zhang, Dianne Cook, Ursula Laa, Nicolas Langrené and Patricia Menéndez 624

volesti: Volume Approximation and Sampling for Convex Polytopes in R
Apostolos Chalkis and Vissarion Fisikopoulos 642

Elliptical Symmetry Tests in R
Slad̄ana Babić, Christophe Ley and Marko Palangetić 661

The vote Package: Single Transferable Vote and Other Electoral Systems in R
Adrian E. Raftery, Hana Ševčíková and Bernard W. Silverman 673

RPESE: Risk and Performance Estimators Standard Errors with Serially Dependent Data
Anthony-Alexander Christidis and R. Douglas Martin 697

RobustBF: An R Package for Robust Solution to the Behrens-Fisher Problem
Gamze Güven, Şükrü Acıtaş, Hatice Şamkar and Birdal Şenoğlu 713

News and Notes

Changes in R
Tomas Kalibera, Sebastian Meyer, Kurt Hornik, Gennadiy Starostin and Luke Tierney 734

Changes on CRAN
Kurt Hornik, Uwe Ligges and Achim Zeileis 738

R Foundation News
Torsten Hothorn 741

News from the Forwards Taskforce
Heather Turner 742

News from the Bioconductor Project
Bioconductor Core Team 744