Reproducible Research with R and RStudio
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1 The R Series Reproducible Research with R and RStudio Christopher Gandrud C\ CRC Press cj* Taylor & Francis Croup Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group an informa business A CHAPMAN & HALL BOOK
2 Contents Preface Stylistic Conventions Required R Packages Additional Resources Chapter Examples Short Example Project List of Figures List of Tables vii xv xvii xix xix xix xxiv xxv I Getting Started 1 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, and RStudio for Reproducible Research? Installing the main software Book Overview How to read this book Reproduce this book Contents overview 16 IX
3 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, & make your files available 25 Getting Started with R, RStudio, and knitr Using R: the Basics Objects Component selection Subscripts Functions and commands Arguments The workspace & history Global R options Installing new packages and loading commands Using RStudio Using knitr: the Basics What knitr does File extensions Code chunks Global chunk options knitr package options Hooks knitr & RStudio knitr & R 55 Getting Started with File Management File Paths & Naming Conventions Root directories Subdirectories & parent directories Spaces in directory & file names Working directories Organizing Your Research Project Setting Directories as RStudio Projects R File Manipulation Commands Unix-like Shell Commands for File Management File Navigation in RStudio 72 Data Gathering and Storage 73
4 5 Storing, Collaborating, Accessing Files, &c Versioning Saving Data in Reproducible Formats Storing Your Files in the Cloud: Dropbox Storage Accessing data 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 Collaboration with GitHub Summing up the GitHub workflow RStudio & GitHub Setting up Git/GitHub with Projects Using Git in RStudio Projects 99 6 Gathering Data with R Organize Your Data Gathering: Makefiles R Make-like files GNU Make Example makefile Makefiles and RStudio Projects Other information about makefiles Importing Locally Stored Data Sets Importing Data Sets from the Internet Data from non-secure (http) URLs Ill Data from secure (https) URLs Ill Compressed data stored online Data APIs & feeds Advanced Automatic Data Gathering: Web Scraping 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 135 xi
5 xii The merge command Duplicate values Duplicate columns 139 III Analysis and Results Statistical Modelling and knitr Incorporating Analyses into the Markup Full code chunks Showing code & results inline LaTeX Markdown Dynamically including non-r code in code chunks Dynamically Including Modular Analysis Files Source from a local file Source from a non-secure URL (http) Source from a secure URL (https) Reproducibly Random: set. seed Computationally Intensive Analyses Showing Results with Tables Basic knitr Syntax for Tables Table Basics Tables in LaTeX Tables in Markdown/HTML Creating Tables from R Objects xtable & apsrtable basics with supported class objects apsrtable for LaTeX xtable with non-supported class objects Creating variable description documents with xtable Showing Results with Figures Including Non-knitted Graphics Including graphics in LaTeX Including graphics in Markdown/HTML Basic knitr Figure Options Chunk options Global options Knitting R's Default Graphics Including ggplot2 Graphics Showing regression results with caterpillar plots JavaScript Graphs with googlevis 198 IV Presentation Documents 203
6 xiii 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 Large LaTeX Documents: Theses, Books, & Batch Reports Planning Large Documents Large Documents with Traditional LaTeX Inputting/including children Other common features of large documents knitr and Large Documents The parent document Knitting child documents Child Documents in a Different Markup Language Creating Batch Reports Presenting on the Web with Markdown The Basics Getting started with Markdown editors Preamble and document structure Headers Horizontal lines Paragraphs and new lines Italics and bold Links Special characters and font customization Lists Escape characters Math with MathJax 245
7 XIV 13.2 Markdown with Pandoc and Custom CSS Pandoc CSS style files and Markdown knitr's pandoc command Slideshows with Markdown, knitr, and HTML Slideshows with Markdown, knitr, and RStudio's R Presentations Slideshows with Markdown, knitr, and slidif y Publishing Markdown Documents Stand alone HTML files Hosting webpages with Dropbox GitHub Pages 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? Bibliography 271 Index 279
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