A peer-reviewed, open-access publication of the
R Foundation for Statistical Computing
Contents
Editorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Contributed Research Articles
iotools: High-Performance I/O Tools for R . . . . . . . . . . . . . . . . . . . 6
IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data
Using R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Network Visualization with ggplot2 . . . . . . . . . . . . . . . . . . . . . . 27
OrthoPanels: An R Package for Estimating a Dynamic Panel Model with Fixed Effects
Using the Orthogonal Reparameterization Approach . . . . . . . . . . . . . . . 60
The mosaic Package: Helping Students to ‘Think with Data’ Using R . . . . . . . . 77
smoof: Single- and Multi-Objective Optimization Test Functions . . . . . . . . . . 103
minval: An R package for MINimal VALidation of Stoichiometric Reactions . . . . . 114
Working with Daily Climate Model Output Data in R and the futureheatwaves Package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
alineR: an R Package for Optimizing Feature-Weighted Alignments and Linguistic
Distances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Implementing a Metapopulation Bass Diffusion Model using the R Package deSolve . 153
MDplot: Visualise Molecular Dynamics. . . . . . . . . . . . . . . . . . . . . 164
On Some Extensions to GA Package: Hybrid Optimisation, Parallelisation and Islands
Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
imputeTS: Time Series Missing Value Imputation in R . . . . . . . . . . . . . . 207
The NoiseFiltersR Package: Label Noise Preprocessing in R . . . . . . . . . . . . 219
coxphMIC: An R Package for Sparse Estimation of Cox Proportional Hazards Models
via Approximated Information Criteria . . . . . . . . . . . . . . . . . . . . . 229
Update of the nlme Package to Allow a Fixed Standard Deviation of the Residual Error239
EMSaov: An R Package for the Analysis of Variance with the Expected Mean Squares
and its Shiny Application . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
GsymPoint: An R Package to Estimate the Generalized Symmetry Point, an Optimal
Cut-off Point for Binary Classification in Continuous Diagnostic Tests. . . . . . . . 262
autoimage: Multiple Heat Maps for Projected Coordinates . . . . . . . . . . . . 284
Market Area Analysis for Retail and Service Locations with MCI . . . . . . . . . . 298
2
PSF: Introduction to R Package for Pattern Sequence Based Forecasting Algorithm . . 324
flan: An R Package for Inference on Mutation Models. . . . . . . . . . . . . . . 334
Multilabel Classification with R Package mlr. . . . . . . . . . . . . . . . . . . 352
Counterfactual: An R Package for Counterfactual Analysis . . . . . . . . . . . . 370
Retrieval and Analysis of Eurostat Open Data with the eurostat Package . . . . . . 385
PGEE: An R Package for Analysis of Longitudinal Data with High-Dimensional
Covariates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393
BayesBinMix: an R Package for Model Based Clustering of Multivariate Binary Data . 403
pdp: An R Package for Constructing Partial Dependence Plots . . . . . . . . . . . 421
checkmate: Fast Argument Checks for Defensive R Programming . . . . . . . . . 437
milr: Multiple-Instance Logistic Regression with Lasso Penalty . . . . . . . . . . 446
spcadjust: An R Package for Adjusting for Estimation Error in Control Charts . . . . 458
Weighted Effect Coding for Observational Data with wec . . . . . . . . . . . . . 477
Hosting Data Packages via drat: A Case Study with Hurricane Exposure Data . . . . 486