Additional Resources / Readings

Example Research Papers

• “Unequal Representation and Gender Stereotypes in Image Search Results for Occupations”
  • example paper (README.Rmd) by Kay, Matthew, Matuszek, Cynthia, and Munson, Sean.
• “Subliminal evaluative conditioning? Above-chance CS identification may be necessary and insufficient for attitude learning”
  • example paper (main.Rmd) by Christoph Stahl, Julia Haaf, and Olivier Corneille

Syntax Guides

• “Markdown Cheatsheet”
  • A guide from Adam Pritchard on formatting of Markdown documents
• “R Markdown Cheatsheet”
  • RStudio-style cheatsheet for R Markdown

Tutorials

• “R Markdown for Scientists”
  • A self-guided tutorial on the essentials of R Markdown reports from Nick Tierney
• R Markdown
  • Multi-part introduction to R Markdown and output formats from R Studio.

Reference

• “Chunk options and package options”
  • Book section from Yihui Xie (creator of R Markdown) on settings to control how knitr runs code chunks.
• “R Markdown: The Definitive Guide”
  • Book from Yihui Xie, J.J. Allaire, and Garrett Grolemund on everything R Markdown.

Formatting Tips

• “How I Teach R Markdown”
  • Blogpost from Alison Hill on teaching Rmarkdown, that nonetheless contains useful tips.
• “kableExtra”
  • Website for the kableExtra package from Hao Zhu, which adds advanced formatting options for tables produced by knitr::kable().
• “stargazer: beautiful LaTeX, HTML and ASCII tables from R statistical output”
  • Vignette from Marek Hlavac on the stargazer package, which produces statistical summary tables (as caommonly seen in academic articles).
• “gt”
  • The gt package for publication-ready tables.
• “flextable”
  • The flextable package for styling tables. Note that flextable includes support for MS Word and PDF outputs, whereas gt currently supports HTML, LaTeX, and RTF output.

Writing Papers

• “papaja: Reproducible APA manuscripts with R Markdown”
  • The papaja package by Frederik Aust & Marius Barth
• “rticles: Article Formats for R Markdown”
  • The rticles package by J. Allaire, Xie, R Foundation, et al., that contains templates for many different journals.
• “RStudio Addin to Insert Markdown Citations”
  • The citr package by Frederik Aust
• Collections of Citation Style Language (.csl) files:
  • https://github.com/citation-style-language/styles
  • https://www.zotero.org/styles

Related Tools

• “thesisdown”
  • R package that extends R Markdown for thesis-specific formatting. Also see Kristen Sauby’s template for UF theses
• “Bookdown”
  • R package that extends R Markdown for book-length outputs, and better figure/table/reference functionality.
• “pkgdown”
  • R package that extends R Markdown for generating documentation websites for R packages (and what this website was created in)
• “blogdown”
  • R package that extends R Markdown for generating personal websites (this guide from Yihui Xie, Amber Thomas, and Alison Presmanes Hill is my recommendation for where to start)
• “Distill for R Markdown”
  • R package for publishing scientific and technical writing to the web (without additional software dependencies), from RStudio folks.
• “Presentation Ninja with xaringan”
  • Slides from Yihui Xie on the xaringan package, for slides rendered using remark.js.