The R Journal, Volume 8/2, December 2016

Complete issue

Complete bibliography

Table of contents

Michael Lawrence 4

Contributed Research Articles

multipleNCC: Inverse Probability Weighting of Nested Case-Control Data
Nathalie C. Støer and Sven Ove Samuelsen 5

QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis
Christopher M. Moore, Christopher R. Stieha, Ben C. Nolting, Maria K. Cameron and Karen C. Abbott 19

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy
Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra and Daniele Ramazzotti 39

diverse: an R Package to Analyze Diversity in Complex Systems
Miguel R. Guevara, Dominik Hartmann and Marcelo Mendoza 60

Simulating Correlated Binary and Multinomial Responses under Marginal Model Specification: The SimCorMultRes Package
Anestis Touloumis 79

eiCompare: Comparing Ecological Inference Estimates across EI and EI:RC
Loren Collingwood, Kassra Oskooii, Sergio Garcia-Rios and Matt Barreto 92

rnrfa: An R package to Retrieve, Filter and Visualize Data from the UK National River Flow Archive
Claudia Vitolo, Matthew Fry and Wouter Buytaert 102

Qtools: A Collection of Models and Tools for Quantile Inference
Marco Geraci 117

Two-Tier Latent Class IRT Models in R
Silvia Bacci and Francesco Bartolucci 139

Variants of Simple Correspondence Analysis
Rosaria Lombardo and Eric J. Beh 167

hdm: High-Dimensional Metrics
Victor Chernozhukov, Chris Hansen and Martin Spindler 185

Normal Tolerance Interval Procedures in the tolerance Package
Derek S. Young 200

easyROC: An Interactive Web-tool for ROC Curve Analysis Using R Language Environment
Dincer Goksuluk, Selcuk Korkmaz, Gokmen Zararsiz and A. Ergun Karaagaoglu 213

tigris: An R Package to Access and Work with Geographic Data from the US Census Bureau
Kyle Walker 231

Escape from Boxland
Barret Schloerke, Hadley Wickham, Dianne Cook and Heike Hofmann 243

Ake: An R Package for Discrete and Continuous Associated Kernel Estimations
Wanbitching E. Wansouwé, Sobom M. Somé and Célestin C. Kokonendji 258

An Introduction to Principal Surrogate Evaluation with the pseval Package
Michael C. Sachs and Erin E. Gabriel 277

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Zinovyev and Eric Bonnet 293

Subgroup Discovery with Evolutionary Fuzzy Systems in R: The SDEFSR Package
Ángel M. García, Francisco Charte, Pedro González, Cristóbal J. Carmona and María J. del Jesus 307

dCovTS: Distance Covariance/Correlation for Time Series
Maria Pitsillou and Konstantinos Fokianos 324

comf: An R Package for Thermal Comfort Studies
Marcel Schweiker 341

water: Tools and Functions to Estimate Actual Evapotranspiration Using Land Surface Energy Balance Models in R
Guillermo Federico Olmedo, Samuel Ortega-Farías, Daniel de la Fuente-Sáiz, David Fonseca- Luego and Fernando Fuentes-Peñailillo 352

quantreg.nonpar: An R Package for Performing Nonparametric Series Quantile Regression
Michael Lipsitz, Alexandre Belloni, Victor Chernozhukov and Iván Fernández-Val 370

nmfgpu4R: GPU-Accelerated Computation of the Non-Negative Matrix Factorization (NMF) Using CUDA Capable Hardware
Sven Koitka and Christoph M. Friedrich 382

Computing Pareto Frontiers and Database Preferences with the rPref Package
Patrick Roocks 393

micompr: An R Package for Multivariate Independent Comparison of Observations
Nuno Fachada, João Rodrigues, Vitor V. Lopes, Rui C. Martins and Agostinho C. Rosa 405

mixtox: An R Package for Mixture Toxicity Assessment
Xiang-Wei Zhu and Jian-Yi Chen 421

Weighted Distance Based Discriminant Analysis: The R Package WeDiBaDis
Itziar Irigoien, Francesc Mestres and Concepcion Arenas 434

Distance Measures for Time Series in R: The TSdist Package
Usue Mori, Alexander Mendiburu and Jose A. Lozano 451

condSURV: An R Package for the Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Luis Meira-Machado and Marta Sestelo 460

ggfortify: Unified Interface to Visualize Statistical Results of Popular R Packages
Yuan Tang, Masaaki Horikoshi and Wenxuan Li 474

Measurement Units in R
Edzer Pebesma, Thomas Mailund and James Hiebert 486

mctest: An R Package for Detection of Collinearity among Regressors
Muhammad Imdadullah, Muhammad Aslam and Saima Altaf 495

News and Notes

R Foundation News
by Torsten Hothorn 506

Changes on CRAN
by Kurt Hornik and Achim Zeileis 507

News from the Bioconductor Project
by Bioconductor Core Team 510

Changes in R
by the R Core Team 511