Reproducible Research with R and RStudio

I Getting Started 
1 Introducing Reproducible Research 
What Is Reproducible Research? 
Why Should Research Be Reproducible? 
For science 
For you 
Who Should Read This Book? 
Academic researchers 
Students 
Instructors 
Editors 
Private sector researchers 
The Tools of Reproducible Research 
Why Use R, knitr/R Markdown, and RStudio for Reproducible Research? 
Installing the main software 
Installing markup languages 
GNU Make 
Other Tools 
Book Overview 
How to read this book 
Reproduce this book 
Contents overview 
2 Getting Started with Reproducible Research 
The Big Picture: A Workflow for Reproducible Research 
Reproducible theory 
Practical Tips for Reproducible Research 
Document everything! 
Everything is a (text) file 
All files should be human readable 
Explicitly tie your files together 
Have a plan to organize, store, and make your files available
3 Getting Started with R, RStudio, and knitr/R Markdown 
Using R: The Basics 
Objects 
Functions 
The workspace & history 
R history 
Global R options 
Installing new packages and loading functions 
Using RStudio 
Using knitr and R Markdown: The basics 
What knitr does 
What rmarkdown does 
File extensions 
Code chunks 
Global chunk options 
knitr package options 
Hooks 
knitr, R Markdown, & RStudio 
knitr & R 
R Markdown and R 
4 Getting Started with File Management 
File Paths & Naming Conventions 
Root directories 
Sub-directories & parent directories 
Working directories 
Absolute vs relative paths 
Spaces in directory & file names 
Organizing Your Research Project 
Organizing Research with RStudio Projects 
R File Manipulation Functions 
Unix-like Shell Commands for File Management 
File Navigation in RStudio 
II Data Gathering and Storage 
5 Storing, Collaborating, Accessing Files, and Versioning 
Saving Data in Reproducible Formats 
Storing Your Files in the Cloud: Dropbox 
Storage 
Accessing data 
Contents v
Collaboration 
Version control 
Storing Your Files in the Cloud: GitHub 
Setting up GitHub: Basic 
Version control with Git 
Remote storage on GitHub 
Accessing on GitHub 
Summing up the GitHub workflow 
RStudio & GitHub 
Setting up Git/GitHub with Projects 
Using Git in RStudio Projects 
6 Gathering Data with R 
Organize Your Data Gathering: Makefiles 
R Make-like files 
GNU Make 
Importing Locally Stored Data Sets 
Importing Data Sets from the Internet 
Data from non-secure (http) URLs 
Data from secure (https) URLs 
Compressed data stored online 
Data APIs & feeds 
Advanced Automatic Data Gathering: Web Scraping 
7 Preparing Data for Analysis 
Cleaning Data for Merging 
Get a handle on your data 
Reshaping data 
Renaming variables 
Ordering data 
Subsetting data 
Recoding string/numeric variables 
Creating new variables from old 
Changing variable types 
Merging Data Sets 
Binding 
Merging data frames 
Duplicate columns 
8 Statistical Modeling and knitr/R Markdown 
Incorporating Analyses into the Markup 
Full code chunks 
Showing code & results inline 
Dynamically including non-R code in code chunks 
vi Contents
Dynamically Including Modular Analysis Files 
Source from a local file 
Source from a URL 
Reproducibly Random: setseed() 
Computationally Intensive Analyses 
9 Showing Results with Tables 
Basic knitr Syntax for Tables 
Table Basics 
Tables in LaTeX 
Tables in Markdown/HTML 
Creating Tables from Supported Class R Objects 
kable for Markdown and LaTeX 
xtable for LaTeX and HTML 
Fitting Large Tables in LaTeX 
xtable with non-supported class objects 
Creating variable description documents with xtable 
10 Showing Results with Figures 
Including Non-knitted Graphics 
Including graphics in LaTeX 
Including graphics in Markdown/HTML 
Non-knitted graphics with knitr/rmarkdown 
Basic knitr/rmarkdown Figure Options 
Chunk options 
Global options 
Knitting R’s Default Graphics 
Including ggplot Graphics 
Showing regression results with caterpillar plots 
JavaScript Graphs with googleVis 
Basic googleVis figures 
Including googleVis in knitted documents 
JavaScript Graphs with htmlwidgets-based packages 
11 Presenting with LaTeX 
The Basics 
Getting started with LaTeX editors 
Basic LaTeX command syntax 
The LaTeX preamble & body 
Headings 
Paragraphs & spacing 
Horizontal lines 
Text formatting 
Math 
Lists 
Footnotes 
Cross-references 
Bibliographies with BibTeX 
The bib file 
Including citations in LaTeX documents 
Generating a BibTeX file of R package citations 
Presentations with LaTeX Beamer 
Beamer basics 
knitr with LaTeX slideshows 
12 Presenting in a Variety of Formats with R Markdown 
The Basics 
Getting started with Markdown editors 
Preamble and document structure 
Headings 
Horizontal lines 
Paragraphs and new lines 
Italics and bold 
Links 
Lists 
Math with MathJax 
Further Customizability with rmarkdown 
CSS style files and Markdown 
Slideshows with Markdown, R Markdown, and HTML 
HTML Slideshows with rmarkdown 
LaTeX Beamer Slideshows with rmarkdown 
Slideshows with Markdown and RStudio’s R Presentations
Publishing HTML Documents Created with R Markdown 
Further information on R Markdown 
13 Conclusion 
Citing Reproducible Research 
Licensing Your Reproducible Research 
Sharing Your Code in Packages 
Project Development: Public or Private? 
Is it Possible to Completely Future-Proof Your Research?