• Reproducible Research in R
    • Learning outcomes
    • Workshop description
    • Prerequisite
    • Keywords
    • Schedule
    • Authors and copyright
  • Part I: Rmarkdown from scratch
  • 1 Markdown syntax
    • 1.1 Introduction
    • 1.2 RStudio tweaks
    • 1.3 Headers
    • 1.4 Bullet points
    • 1.5 Task list
    • 1.6 Code and Math blocks
      • 1.6.1 Code chunk
      • 1.6.2 Math chunk
    • 1.7 Images
    • 1.8 Final look
  • 2 YAML header
    • 2.1 Introduction
      • 2.1.1 Example 1 (Correct YAML)
      • 2.1.2 Example 2 (Correct YAML)
      • 2.1.3 Example 3 (Incorrect YAML)
    • 2.2 Title, date and author keys
    • 2.3 Output key
    • 2.4 Configuring output document
    • 2.5 Final look
  • 3 The code chunks
    • 3.1 Introduction
    • 3.2 Chunk name
    • 3.3 Chunk options
    • 3.4 Message and warning options
    • 3.5 More code chunks and data wragnling
    • 3.6 Session info
    • 3.7 Setup chunk
    • 3.8 Final look
  • 4 Extras
    • 4.1 Code folding
    • 4.2 Presentation slides (ioslides)
    • 4.3 ioslides features
    • 4.4 Tabs
      • 4.4.1 Final look
  • Part II: Git, GitHub and RStudio Rproj file
  • 5 Git (part one)
    • 5.1 Introduction
    • 5.2 Git init
    • 5.3 Git commit
    • 5.4 Git username and useremail
  • 6 GitHub (part one)
    • 6.1 Introduction
    • 6.2 New repository
    • 6.3 Repository address (git remote`)
    • 6.4 Linking Git with GitHub
  • 7 Git (part two)
    • 7.1 Introduction
    • 7.2 Linking Git with GitHub (repeat)
    • 7.3 “origin” lingo in git
    • 7.4 git push
    • 7.5 git pull
  • 8 GitHub (part two)
    • 8.1 README.md
    • 8.2 GitHub pages (gh-pages)
    • 8.3 Visible contributions
  • Part III: Text referencing, Cross referencing and Citation
  • 9 Text referencing
    • 9.1 Introduction
      • 9.1.1 Starting blob of text (optional)
      • 9.1.2 Linking
    • 9.2 bookdown::html_document2
    • 9.3 Creating labels
    • 9.4 Using labels
    • 9.5 Cross referencing
  • 10 Citations
    • 10.1 Introductions
    • 10.2 BibTex
      • 10.2.1 Introduction
      • 10.2.2 knitr::write_bib
      • 10.2.3 BibTex keys
    • 10.3 Where do I get .bib file?
      • 10.3.1 Citation managment software
      • 10.3.2 ZoteroBib service
      • 10.3.3 RefMangeR
      • 10.3.4 Journal websites
    • 10.4 Linking .bib file with Rmarkdown document
    • 10.5 Inline citation
    • 10.6 References section
    • 10.7 Citation style
    • 10.8 Linking inline citation with the references list
    • 10.9 Footnotes
    • 10.10 Citr addin
  • Part IV: Static, multi-paged website with rmarkdown and bookdown
  • 11 Static website
    • 11.1 Introduction
    • 11.2 Build tools setup
    • 11.3 First three files
    • 11.4 Output directory name
    • 11.5 More content
  • 12 Bookdown
    • 12.1 Introduction
    • 12.2 Masking files
    • 12.3 Adding section headers
    • 12.4 Bookdown skeleton
      • 12.4.1 Apporach 1
      • 12.4.2 Approach 2
  • Appendix
  • A Resources

Reproducible Research in R

A Resources

  • knitr vs rmarkdown vs bookdown

  • Happy Git and GitHub for the useR

  • RMarkdown for Scientists by Nicholas Tierney

  • related stackoverflow question

  • Presentation slides on Rmarkdown ecosystem

  • R chunks

  • Here is nice cheatsheet that has comprehensive cover of all the options you can pass in.

    https://eddjberry.netlify.com/post/writing-your-thesis-with-bookdown/ https://rmarkdown.rstudio.com/lesson-9.html https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html

  • Section 2.6

  • Pimp my RMD

    https://crsh.github.io/papaja_man/r-markdown-components.html#yaml-front-matter

    https://kbroman.org/knitr_knutshell/ http://leisch.userweb.mwn.de/Sweave/

  • section 10: Which files to commit from here