Learning RStudio for R Statistical Computing

126 Pages·2012·10.42 MB·English

by  Mark P.J. van der Loo

Learning RStudio for
R Statistical Computing
Learn to effectively perform R development, statistical
analysis, and reporting with the most popular R IDE
Mark P.J. van der Loo
Edwin de Jonge
BIRMINGHAM - MUMBAI
Learning RStudio for R Statistical Computing
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First published: December 2012
Production Reference: 1171212
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ISBN 978-1-78216-060-1
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Cover Image by Tarun Singh ([e-mail])
Credits
Authors Project Coordinator
Mark P.J. van der Loo Esha Thakker
Edwin de Jonge
Proofreader
Maria Gould
Reviewers
Mzabalazo Z. Ngwenya
Yihui Xie Indexer
Monica Ajmera Mehta
Acquisition Editor
Kartikey Pandey Production Coordinator
Prachali Bhiwandkar
Commissioning Editor
Meeta Rajani Cover Work
Prachali Bhiwandkar
Technical Editors
Prasad Dalvi
Pooja Pande
About the Authors
Mark P.J. van der Loo obtained his PhD from the Institute for Theoretical
Chemistry at the University of Nijmegen (The Netherlands). Since 2007 he has
worked at the statistical methodology department of the Dutch official statistics
office (Statistics Netherlands). His research interests include automated data cleaning
methods and statistical computing. At Statistics Netherlands he is responsible for
the local R center of expertise, which supports and educates users on statistical
computing with R. Mark has been teaching R for several years and (co)authored a
number of R packages that are available via CRAN: editrules, deducorrect, rspa, and
extremevalues. A list of publications can be found at www.markvanderloo.eu.
Edwin de Jonge has worked for more than 15 years at the Dutch official statistics
office (Statistics Netherlands). Having a background in theoretical and computational
solid state physics (MSc.) he started working at the statistical computing department.
Currently he works with the statistical methodology department. His research
interests include data visualization, data analysis, and statistical computing. He has
trained over 150 people in the workshop Graphical Analysis with R. Edwin has (co)
authored several R packages that are available via CRAN: tabplot, tabplotd3, ffbase,
whisker, editrules, and deducorrect.
About the Reviewers
Mzabalazo Z. Ngwenya has worked extensively in the field of consulting and
currently works as a biometrician.
Yihui Xie (http://yihui.name) is currently a PhD student in the Department of
Statistics, Iowa State University. His research interests include interactive statistical
graphics, statistical computing, and reproducible research. He is the author of several
R packages such as animation, cranvas, formatR, Rd2roxygen, and knitr, among which
the animation package won the 2009 John M. Chambers Statistical Software Award
(American Statistical Association). In 2006 he founded the Capital of Statistics
(http://cos.name), which has grown into a large online community on statistics in
China. He also initiated the first Chinese R conference in 2008 and has been organizing
R conferences in China since then. He is a co-author of the book Reproducible Research
with R (Chapman & Hall), which is under development.
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Table of Contents
Preface 1
Chapter 1: Getting Started 5
RStudio at a glance 7
Installing RStudio 9
Installing R 9
Installing R on Windows and Mac OS X 9
Installing R on Linux 9
Building R from source 10
Building R using Windows 11
Installing RStudio 11
Installing RStudio Server 11
Installing R packages 11
Overview: A first R session 12
Keyboard shortcuts 17
Getting help 17
What if I uninstall RStudio? 18
Further reading 18
Summary 19
Chapter 2: Writing R Scripts and the R Console 21
Moving around RStudio 21
Features of the R console 23
Executing commands 23
Command history 24
Command completion 26
Completion of functions and arguments 27
Object completion 28
Completion of filenames 28
Keyboard shortcuts for the console 29
Table of Contents
Features of the source editor 30
Editing R scripts 31
Syntax highlighting 33
Indenting code 35
Commenting code 35
Find and replace 36
Folding, sectioning, and navigation 37
Code folding 37
Code navigation 37
Code sections 39
Code execution 40
Summary 41
Chapter 3: Viewing and Plotting Data 43
Viewing data and the object browser 43
Plotting 46
Zoom 46
Export 47
Navigation 48
Interactive plotting with the manipulate package 48
The manipulate function 48
Using more options of manipulate 50
Advanced topic: retrieving plot parameters from manipulate 51
Summary 55
Chapter 4: Managing R Projects 57
R projects 57
Creating an R project 58
Directory structure and file manipulations 59
Version control 60
Introduction to version control 60
Installing GIT or Subversion 61
Version control for single-person projects 62
GIT 62
Subversion 68
Working with a team 73
Further reading 74
Summary 74
Chapter 5: Generating Reports 75
Prerequisites for report generation 76
Notebook 77
Notebook options 77
Publishing a notebook 79
[ ii ]
Table of Contents
R Markdown and Rhtml 79
Workflow for R Markdown 79
An extended example 80
An introduction to Markdown syntax 84
Rhtml 85
Code chunks 85
Chunk syntax and options 86
RMarkdown: .Rmd files 86
Rhtml: .Rhtml files 86
LaTeX: .Rnw files 86
RStudio's chunk support and keyboard shortcuts 88
LaTeX 89
Further reading 91
Summary 91
Chapter 6: Using RStudio Effectively 93
Additional features for function writing 93
Function extraction 94
Function navigation 95
Introduction to package writing 97
Prerequisites 98
Basic structure and workflow 98
Creating the package directory structure 99
Documenting functions with Roxygen2 99
Building your package with devtools 101
More about the devtools package 102
Publishing your package 102
Summary 103
Index 105
[ iii ]