Appendix F. Packages used in this book
R derives much of its breadth and power from the contributions of selfless authors. Table F.1 lists the user-contributed packages described in this book, along with the chapter(s) in which they appear.
Table F.1. Contributed packages used in this book
|
Package |
Authors |
Description |
Chapters |
|---|---|---|---|
| AER | Christian Kleiber and Achim Zeileis | Functions, data sets, examples, demos, and vignettes from the book Applied Econometrics with R by Christian Kleiber and Achim Zeileis | 13 |
| Amelia | James Honaker, Gary King, and Matthew Blackwell | Amelia II: A program for missing data via multiple imputation | 15 |
| arrayImpute | Eun-kyung Lee, Dankyu Yoon, and Taesung Park | Missing imputation for microarray data | 15 |
| arrayMissPattern | Eun-kyung Lee andTaesung Park | Exploratory analysis of missing patterns for microarray data | 15 |
| boot | S original by Angelo Canty. R port by Brian Ripley. | Bootstrap functions | 12 |
| ca | Michael Greenacre and Oleg Nenadic | Simple, multiple and joint correspondence analysis | 7 |
| car | John Fox and Sanford Weisberg | Companion to Applied Regression | 1, 8, 9, 10, 11 |
| cat | Ported to R by Ted Harding and Fernando Tusell. Original by Joseph L. Schafer. | Analysis of categorical-variable datasets with missing values | 15 |
| coin | Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel, and Achim Zeileis | Conditional inference procedures in a permutation test framework | 12 |
| corrgram | Kevin Wright | Plot a correlogram | 11 |
| corrperm | Douglas M. Potter | Permutation tests of correlation with repeated measurements | 12 |
| doBy | SØren HØjsgaard with contributions from Kevin Wright and Alessandro A. Leidi. | Group-wise computations of summary statistics, general linear contrasts and other utilities | 7 |
| effects | John Fox and Jangman Hong | Effect displays for linear, generalized linear, multinomial-logit, and proportional-odds logit models | 8, 9 |
| FactoMineR | Francois Husson, Julie Josse, Sebastien Le, and Jeremy Mazet | Multivariate exploratory data analysis and data mining with R | 14 |
| FAiR | Ben Goodrich | Factor analysis using a genetic algorithm | 14 |
| fCalendar | Diethelm Wuertz and Yohan Chalabi | Functions for chronological and calendarical objects | 4 |
| foreign | R-core members, Saikat DebRoy, Roger Bivand, and others | Read data stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, and others | 2 |
| gclus | Catherine Hurley | Clustering graphics | 1, 11 |
| ggplot2 | Hadley Wickam | An implementation of the Grammar of Graphics | 16 |
| glmPerm | Wiebke Werft and Douglas M. Potter | Permutation test for inference in generalized linear models | 12 |
| gmodels | Gregory R. Warnes. Includes R source code and/or documentation contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson. Contributions from Randall C. Johnson are Copyright (2005) SAIC-Frederick, Inc. | Various R programming tools for model fitting | 7 |
| gplots | Gregory R. Warnes. Includes R source code and/or documentation contributed by Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, and Bill Venables | Various R programming tools for plotting data | 6, 9 |
| grid | Paul Murrell | A rewrite of the graphics layout capabilities, plus some support for interaction | 16 |
| gvlma | Edsel A. Pena and Elizabeth H. Slate | Global validation of linear models assumptions | 8 |
| hdf5 | Marcus G. Daniels | Interface to the NCSA HDF5 library | 2 |
| hexbin | Dan Carr, ported by Nicholas Lewin-Koh and Martin Maechler | Hexagonal binning routines | 11 |
| HH | Richard M. Heiberger | Support software for Statistical Analysis and Data Display by Heiberger andHolland | 9 |
| Hmisc | Frank E Harrell Jr, with contributions from many other users | Harrell miscellaneous functions for data analysis, high-level graphics, utility operations, and more | 2, 3, 7 |
| kmi | Arthur Allignol | Kaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting | 15 |
| lattice | Deepayan Sarkar | Lattice graphics | 16 |
| latticist | Felix Andrews | GUI for exploratory visualization | 16 |
| lavaan | Yves Rosseel | Functions for latent variable models, including confirmatory factor analysis, structural equation modeling, and latent growth curve models | 14 |
| lcda | Michael Buecker | Latent class discriminant analysis | 14 |
| leaps | Thomas Lumley using Fortran code by Alan Miller | Regression subset selection including exhaustive search | 8 |
| lmPerm | Bob Wheeler | Permutation tests for linear models | 12 |
| logregperm | Douglas M. Potter | Permutation test for inference in logistic regression | 12 |
| longitudinalData | Christophe Genolini | Tools for longitudinal data | 15 |
| lsa | Fridolin Wild | Latent semantic analysis | 14 |
| ltm | Dimitris Rizopoulos | Latent trait models under item response theory | 14 |
| lubridate | Garrett Grolemund and Hadley Wickham | Functions to identify and parse date-time data, extract and modify components of a date-time, perform accurate math on date-times, and handle time zones and Daylight Savings Time | 4 |
| MASS | S original by Venables and Ripley. R port by Brian Ripley, following earlier work by Kurt Hornik and Albrecht Gebhardt. | Functions and datasets to support Venables and Ripley’s Modern Applied Statistics with S (4th edition) | 4, 5, 7, 8, 9, 12 |
| mlogit | Yves Croissant | Estimation of the multinomial logit model | 13 |
| multcomp | Torsten Hothorn, Frank Bretz Peter Westfall, Richard M. Heiberger, and Andre Schuetzenmeister | Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models | 9, 12 |
| mvnmle | Kevin Gross, with help from Douglas Bates | ML estimation for multivariate normal data with missing values | 15 |
| mvoutlier | Moritz Gschwandtner and Peter Filzmoser | Multivariate outlier detection based on robust methods | 9 |
| ncdf, ncdf4 | David Pierce | Interface to Unidata netCDF data files | 2 |
| nFactors | Gilles Raiche | Parallel analysis and non graphical solutions to the Cattell scree test | 14 |
| npmc | Joerg Helms and Ullrich Munzel | Nonparametric multiple comparisons | 7 |
| OpenMx | Steven Boker, Michael Neale, Hermine Maes, Michael Wilde, Michael Spiegel, Timothy R. Brick, Jeffrey Spies, Ryne Estabrook, Sarah Kenny, Timothy Bates, Paras Mehta, and John Fox | Advanced structural equation modeling. | 14 |
| pastecs | Frederic Ibanez, Philippe Grosjean, and Michele Etienne | Package for the analysis of space-time ecological series | 7 |
| piface | Russell Lenth, R package interface by TobiasVerbeke | Java applets for power and sample size assessment | 10 |
| playwith | Felix Andrews | A GTK+ graphical user interface for editing and interacting with R plots | 16 |
| poLCA | Drew Linzer and Jeffrey Lewis | Polytomous variable latent class analysis | 14 |
| psych | William Revelle | Procedures for psychological, psychometric, and personality research | 7, 14 |
| pwr | Stephane Champely | Basic functions for power analysis | 10 |
| qcc | Luca Scrucca | Quality control charts | 13 |
| randomLCA | Ken Beath | Random effects latent class analysis | 14 |
| Rcmdr | John Fox, with contributions from Liviu Andronic, Michael Ash, Theophilius Boye, Stefano Calza, Andy Chang, Philippe Grosjean, Richard Heiberger, G. Jay Kerns, Renaud Lancelot, Matthieu Lesnoff, Uwe Ligges, Samir Messad, Martin Maechler, Robert Muenchen, Duncan Murdoch, Erich Neuwirth, Dan Putler, Brian Ripley, Miroslav Ristic, and PeterWolf. | R Commander, a platform-independent basic-statistics graphical user interface for R, based on the tcltk package | 11 |
| reshape | Hadley Wickham | Flexibly reshape data | 4, 5, 7 |
| rggobi | Duncan Temple Lang, Debby Swayne, Hadley Wickham, and Michael Lawrence | An interface between R and GGobi | 16 |
| rgl | Daniel Adler and Duncan Murdoch | 3D visualization device system (OpenGL) | 11 |
| RJDBC | Simon Urbanek | Provides access to databases through the JDBC interface | 2 |
| rms | Frank E. Harrell, Jr. | Regression modeling strategies - about 225 function that assist with and streamline regression modeling, testing, estimations, validation, graphics, prediction, and typesetting | 13 |
| robust | Jiahui Wang, Ruben Zamar, Alfio Marazzi, Victor Yohai, Matias Salibian-Barrera, Ricardo Maronna, Eric Zivot, David Rocke, Doug Martin, Martin Maechler, and Kjell Konis | A package of robust methods | 13 |
| RODBC | Brian Ripley and Michael Lapsley | ODBC database access | 2 |
| ROracle | David A. James and Jake Luciani | Oracle database interfacefor R | 2 |
| rrcov | Valentin Todorov | Robust location and scatter estimation and robust multivariate analysis with high breakdown point | 9 |
| sampling | Yves Tillé and Alina Matei | Functions for drawing and calibrating samples | 4 |
| scatterplot3d | Uwe Ligges | Plots a three dimensional (3D) point cloud | 11 |
| sem | John Fox with contributions from Adam Kramer and Michael Friendly | Structural equation models | 14 |
| SeqKnn | Ki-Yeol Kim and Gwan-Su Yi, CSBio lab., Information and Communications University | Sequential KNN imputation method | 15 |
| sm | Adrian Bowman and Adelchi Azzalini. Ported to R by B. D. Ripley up to version 2.0, version 2.1 by Adrian Bowman and Adelchi Azzalini, version 2.2 by Adrian Bowman. | Smoothing methods for nonparametric regression and density estimation | 6, 9 |
| vcd | David Meyer, Achim Zeileis, and Kurt Hornik | Functions for visualizing categorical data | 1, 6, 7, 11, 12 |
| vegan | Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, R. B. O’Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, and Helene Wagner | Ordination methods, diversity analysis, and other functions for community and vegetation ecologists | 9 |
| VIM | Matthias Templ, Andreas Alfons, and Alexander Kowarik | Visualization and imputation of missing values | 15 |
| xlsx | Adrian A. Dragulescu | Read, write, and format Excel2007 (xlsx) files | 2 |
| XML | Duncan Temple Lang | Tools for parsing and generating XML within R andS-Plus | 2 |
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