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Reproducible research with R and RStudio / Christopher Gandrud, Hertie School of Governance, Berlin, Germany
Books/Textual Material | CRC Press, Taylor & Francis Group | 2015 | Second edition.
Available at Gumberg 2nd Floor (Q180.55.S7 G36 2015)
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Imprint
Boca Raton : CRC Press, Taylor & Francis Group, [2015]
©2015
Descript
xxvii, 295 pages : illustrations ; 23 cm.
text txt rdacontent
unmediated n rdamedia
volume nc rdacarrier
Series
Note
"A Chapman & Hall book."
Bibliog.
Includes bibliographical references (pages 277-283) and index.
Contents
Machine-generated contents note: 1. Introducing Reproducible Research -- 1.1. What Is Reproducible Research? -- 1.2. Why Should Research Be Reproducible? -- 1.2.1. For science -- 1.2.2. For you -- 1.3. Who Should Read This Book? -- 1.3.1. Academic researchers -- 1.3.2. Students -- 1.3.3. Instructors -- 1.3.4. Editors -- 1.3.5. Private sector researchers -- 1.4. The Tools of Reproducible Research -- 1.5. Why Use R, knitr I markdown, and RStudio for Reproducible Research? -- 1.5.1. Installing the main software -- 1.6. Book Overview -- 1.6.1. How to read this book -- 1.6.2. Reproduce this book -- 1.6.3. Contents overview -- 2. Getting Started with Reproducible Research -- 2.1. The Big Picture: A Workflow for Reproducible Research -- 2.1.1. Reproducible theory -- 2.2. Practical Tips for Reproducible Research -- 2.2.1. Document everything! -- 2.2.2. Everything is a (text) file -- 2.2.3. All files should be human readable -- 2.2.4. Explicitly tie your files together -- 2.2.5. Have a plan to organize, store, and make your files available -- 3. Getting Started with R, RStudio, and knitr/rmarkdown -- 3.1. Using R: The Basics -- 3.1.1. Objects -- 3.1.2. Component selection -- 3.1.3. Subscripts -- 3.1.4. Functions and commands -- 3.1.5. Arguments -- 3.1.6. The workspace & history -- 3.1.7. Global R options -- 3.1.8. Installing new packages and loading functions -- 3.2. Using RStudio -- 3.3. Using knitr and rmarkdown: The Basics -- 3.3.1. What knitr does -- 3.3.2. What rmarkdown does -- 3.3.3. File extensions -- 3.3.4. Code chunks -- 3.3.5. Global chunk options -- 3.3.6. knitr package options -- 3.3.7. Hooks -- 3.3.8. knitr, rmarkdown, & RStudio -- 3.3.9. knitr & R -- 3.3.10. rmarkdown and R -- 4. Getting Started with File Management -- 4.1. File Paths & Naming Conventions -- 4.1.1. Root directories -- 4.1.2. Subdirectories & parent directories -- 4.1.3. Working directories -- 4.1.4. Absolute vs. relative paths -- 4.1.5. Spaces in directory & file names -- 4.2. Organizing Your Research Project -- 4.3. Setting Directories as RStudio Projects -- 4.4. R File Manipulation Commands -- 4.5. Unix-like Shell Commands for File Management -- 4.6. File Navigation in RStudio -- 5. Storing, Collaborating, Accessing Files, and Versioning -- 5.1. Saving Data in Reproducible Formats -- 5.2. Storing Your Files in the Cloud: Dropbox -- 5.2.1. Storage -- 5.2.2. Accessing data -- 5.2.3. Collaboration -- 5.2.4. Version control -- 5.3. Storing Your Files in the Cloud: GitHub -- 5.3.1. Setting up GitHub: Basic -- 5.3.2. Version control with Git -- 5.3.3. Remote storage on GitHub -- 5.3.4. Accessing on GitHub -- 5.3.4.1. Collaboration with GitHub -- 5.3.5. Summing up the GitHub workflow -- 5.4. RStudio & GitHub -- 5.4.1. Setting up Git/GitHub with Projects -- 5.4.2. Using Git in RStudio Projects -- 6. Gathering Data with R -- 6.1. Organize Your Data Gathering: Makefiles -- 6.1.1. R Make-like files -- 6.1.2. GNU Make -- 6.1.2.1. Example makefile -- 6.1.2.2. Makefiles and RStudio Projects -- 6.1.2.3. Other information about makefiles -- 6.2. Importing Locally-Stored Data Sets -- 6.3. Importing Data Sets from the Internet -- 6.3.1. Data from non-secure (http) URLs -- 6.3.2. Data from secure (https) URLs -- 6.3.3. Compressed data stored online -- 6.3.4. Data APIs & feeds -- 6.4. Advanced Automatic Data Gathering: Web Scraping -- 7. Preparing Data for Analysis -- 7.1. Cleaning Data for Merging -- 7.1.1. Get a handle on your data -- 7.1.2. Reshaping data -- 7.1.3. Renaming variables -- 7.1.4. Ordering data -- 7.1.5. Subsetting data -- 7.1.6. Recoding string/numeric variables -- 7.1.7. Creating new variables from old -- 7.1.8. Changing variable types -- 7.2. Merging Data Sets -- 7.2.1. Binding -- 7.2.2. The merge command -- 7.2.3. Duplicate values -- 7.2.4. Duplicate columns -- 8. Statistical Modelling and knitr -- 8.1. Incorporating Analyses into the Markup -- 8.1.1. Full-code chunks -- 8.1.2. Showing code & results inline -- 8.1.2.1. LaTeX -- 8.1.2.2. Markdown -- 8.1.3. Dynamically including non-R code in code chunks -- 8.2. Dynamically Including Modular Analysis Files -- 8.2.1. Source from a local file -- 8.2.2. Source from a non-secure URL (http) -- 8.2.3. Source from a secure URL (https) -- 8.3. Reproducibly Random: set.seed -- 8.4. Computationally-Intensive Analyses -- 9. Showing Results with Tables -- 9.1. Basic knitr Syntax for Tables -- 9.2. Table Basics -- 9.2.1. Tables in LaTeX -- 9.2.2. Tables in Markdown/HTML -- 9.3. Creating Tables from Supported Class R Objects -- 9.3.1. kable for Markdown and LaTeX -- 9.3.2. xtable for LaTeX and HTML -- 9.3.3. texreg for LaTeX and HTML -- 9.3.4. Fitting Large Tables in LaTeX -- 9.3.5. xtable with non-supported class objects -- 9.3.6. Creating variable description documents with xtable -- 10. Showing Results with Figures -- 10.1. Including Non-knitted Graphics -- 10.1.1. Including graphics in LaTeX -- 10.1.2. Including graphics in Markdown/HTML -- 10.2. Basic knitr/rmarkdown Figure Options -- 10.2.1. Chunk options -- 10.2.2. Global options -- 10.3. Knitting R's Default Graphics -- 10.4. Including ggplot2 Graphics -- 10.4.1. Showing regression results with caterpillar plots -- 10.5. JavaScript Graphs with googleVis -- 10.5.1. JavaScript Graphs with html widgets-based packages -- 11. Presenting with knitr/LaTeX -- 11.1. The Basics -- 11.1.1. Getting started with LaTeX editors -- 11.1.2. Basic LaTeX command syntax -- 11.1.3. The LaTeX preamble & body -- 11.1.4. Headings -- 11.1.5. Paragraphs & spacing -- 11.1.6. Horizontal lines -- 11.1.7. Text formatting -- 11.1.8. Math -- 11.1.9. Lists -- 11.1.10. Footnotes -- 11.1.11. Cross-references -- 11.2. Bibliographies with BibTeX -- 11.2.1. The . bib file -- 11.2.2. Including citations in LaTeX documents -- 11.2.3. Generating a BibTeX file of R package citations -- 11.3. Presentations with LaTeX Beamer -- 11.3.1. Beamer basics -- 11.3.2. knitr with LaTeX slideshows -- 12. Large knitr/LaTeX Documents: Theses, Books, and Batch Reports -- 12.1. Planning Large Documents -- 12.2. Large Documents with Traditional LaTeX -- 12.2.1. Inputting/including children -- 12.2.2. Other common features of large documents -- 12.3. knitr and Large Documents -- 12.3.1. The parent document -- 12.3.2. Knitting child documents -- 12.4. Child Documents in a Different Markup Language -- 12.5. Creating Batch Reports -- 13. Presenting on the Web and Other Formats with R Markdown -- 13.1. The Basics -- 13.1.1. Getting started with Markdown editors -- 13.1.2. Preamble and document structure -- 13.1.3. Headings -- 13.1.4. Horizontal lines -- 13.1.5. Paragraphs and new lines -- 13.1.6. Italics and bold -- 13.1.7. Links -- 13.1.8. Special characters and font customization -- 13.1.9. Lists -- 13.1.10. Escape characters -- 13.1.11. Math with MathJax -- 13.2. Further Customizability with rmarkdown -- 13.2.1. More on rmarkdown Headers -- 13.2.2. CSS style files and Markdown -- 13.3. Slideshows with Markdown, rmarkdown, and HTML -- 13.3.1. HTML Slideshows with rmarkdown -- 13.3.2. LaTeX Beamer Slideshows with rmarkdown -- 13.3.3. Slideshows with Markdown and RStudio's R Presentations -- 13.4. Publishing HTML Documents Created by R Markdown -- 13.4.1. Standalone HTML files -- 13.4.2. Hosting webpages with Dropbox -- 13.4.3. GitHub Pages -- 13.4.4. Further information on R Markdown -- 14. Conclusion -- 14.1. Citing Reproducible Research -- 14.2. Licensing Your Reproducible Research -- 14.3. Sharing Your Code in Packages -- 14.4. Project Development: Public or Private? -- 14.5. Is it Possible to Completely Future-Proof Your Research?.
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Reproducible research with R and R Studio
ISBN
9781498715379 (pbk. ; alk. paper)
1498715370 (pbk. ; alk. paper)
MARC
OCoLC
20180531102750.0
150803t20152015flua b 001 0 eng cam i
900624543
DLC eng rda DLC YDXCP BTCTA BDX MBB CHVBK OCLCF OCLCQ QGK CSAIL MNU OCLCO OCLCA DUQ
(OCoLC)915774606 (OCoLC)900624543
DUQQ vmh
pcc
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