Reproducible research with R and RStudio

Author(s)

    • Gandrud, Christopher

Bibliographic Information

Reproducible research with R and RStudio

Christopher Gandrud

（The R series）

CRC Press, c2014

  • : pbk

Available at  / 4 libraries

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Note

Includes bibliographical references (p. 271-277) and index

Description and Table of Contents

Description

Bringing together computational research tools in one accessible source, Reproducible Research with R and RStudio guides you in creating dynamic and highly reproducible research. Suitable for researchers in any quantitative empirical discipline, it presents practical tools for data collection, data analysis, and the presentation of results. With straightforward examples, the book takes you through a reproducible research workflow, showing you how to use: R for dynamic data gathering and automated results presentation knitr for combining statistical analysis and results into one document LaTeX for creating PDF articles and slide shows, and Markdown and HTML for presenting results on the web Cloud storage and versioning services that can store data, code, and presentation files; save previous versions of the files; and make the information widely available Unix-like shell programs for compiling large projects and converting documents from one markup language to another RStudio to tightly integrate reproducible research tools in one place Whether you're an advanced user or just getting started with tools such as R and LaTeX, this book saves you time searching for information and helps you successfully carry out computational research. It provides a practical reproducible research workflow that you can use to gather and analyze data as well as dynamically present results in print and on the web. Supplementary files used for the examples and a reproducible research project are available on the author's website.

Table of Contents

Getting Started Introducing Reproducible Research What Is Reproducible Research? Why Should Research Be Reproducible? Who Should Read This Book? The Tools of Reproducible Research Why Use R, knitr, and RStudio for Reproducible Research? Book Overview Getting Started with Reproducible Research The Big Picture: A Workflow for Reproducible Research Practical Tips for Reproducible Research Getting Started with R, RStudio, and knitr Using R: The Basics Using RStudio Using knitr: The Basics Getting Started with File Management File Paths and Naming Conventions Organizing Your Research Project Setting Directories as RStudio Projects R File Manipulation Commands Unix-like Shell Commands for File Management File Navigation in RStudio Data Gathering and Storage Storing, Collaborating, Accessing Files, and Versioning Saving Data in Reproducible Formats Storing Your Files in the Cloud: Dropbox Storing Your Files in the Cloud: GitHub RStudio and GitHub Gathering Data with R Organize Your Data Gathering: Makefiles Importing Locally Stored Data Sets Importing Data Sets from the Internet Advanced Automatic Data Gathering: Web Scraping Preparing Data for Analysis Cleaning Data for Merging Merging Data Sets Analysis and Results Statistical Modeling and knitr Incorporating Analyses into the Markup Dynamically Including Modular Analysis Files Reproducibly Random: set.seed Computationally Intensive Analyses Showing Results with Tables Basic knitr Syntax for Tables Table Basics Creating Tables from R Objects Showing Results with Figures Including Non-knitted Graphics Basic knitr Figure Options Knitting R's Default Graphics Including ggplot2 Graphics JavaScript graphs with googleVis Presentation Documents Presenting with LaTeX The Basics Bibliographies with BibTeX Presentations with LaTeX Beamer Large LaTeX Documents: Theses, Books, and Batch Reports Planning Large Documents Large Documents with Traditional LaTeX knitr and Large Documents Child Documents in a Different Markup Language Creating Batch Reports Presenting on the Web with Markdown The Basics Markdown with Pandoc and Custom CSS Slideshows with Markdown, knitr, and HTML Publishing Markdown Documents 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 Index

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