R Markdown advanced

A powerful and amazing tool for academic communication

Dr. Peng Zhao (✉ peng.zhao@xjtlu.edu.cn)

Department of Health and Environmental Sciences
Xi’an Jiaotong-Liverpool University

1 Learning objectives

  • Generate academic manuscripts, theses, and slides with R Markdown.
  • Present statistics results in statements, tables, and graphs.
  • Use cross references in scientific writing.

2 Forms of Academic communication

Forms Description Advantages Limitation
Talks Presenting data orally, usually with slides. Vivid with animations and universal in various occasions. Time limit. Electronic devices based. Dependence on the presenter’s improvisation.
Journal papers Presenting data with a completed study and published it in a academic journal. Professional, detailed, strict, and structured. Requirement changes over publishers. Less interaction with readers.
Posters Presenting data with a designed poster and discuss it with other people. Convenient, instant with interaction. Space limit. Dependence on the presenter’s explanation.

R Markdown family:

2.1 Report

2.1.1 The default settings

2.1.2 The prettydoc package

  • Installation
install.packages('prettydoc')

  • Create: RStudio - File - New File - R Markdown - From Template - Lightweight and Pretty Document (HTML) (prettydoc)

  • Knit into .html

2.2 Journal paper

2.2.1 The rticles package

  • Create: RStudio - File - New File - R Markdown - From Template - Elsevier Journal Article (rticles)
  • Knit into .pdf

2.3 Thesis

2.3.1 The bookdown package

  • Create a bookdown project: RStudio - File - New Project - New Directory - Book project using bookdown
  • Build the book

2.4 Slides

2.4.1 The default settings

  • Create: RStudio - New File - R Markdown - Presentation
  • Knit it into .html, .pdf, .pptx

2.4.2 The xaringan package

  • Create: RStudio - File - New File - R Markdown - From Template - Ninja Presentation (xaringan)
  • Knit into .pdf

2.5 More

  • Journal paper: RStudio —> File —> New File —> R Markdown —> From Template
  • Dissertation/book: RStudio: File ➞ New Project ➞ New Directory ➞ Book Project using bookdown
  • slides: RStudio: File ➞ New File ➞ R Markdown ➞ From Template ➞ Ninja Presentation
  • Poster: RStudio: File ➞ New File ➞ R Markdown ➞ From Template ➞ drposter Poster
  • Website: RStudio: File ➞ New Project ➞ New Directory ➞ Website using blogdown
  • CV
  • Letter
  • Music
  • Chess
  • Mindmap
  • …

3 R Markdown header

Output:

output: 
  bookdown::pdf_book: default
  bookdown::html_document2: default
  bookdown::word_document2: default

Titles:

title: Presenting statistical results
subtitle: A demonstration for R Markdown
author: Peng Zhao

Table of contents:

toc: false
lot: false
lof: false

Citations:

link-citations: true
colorlinks: yes  
bibliography: references.bib

4 Presenting statistical results

Demo.

5 Citations & references

  • Bibliography library: .bib
  1. Use Google/Baidu/Bing Scholar for searching a topic of your interest, and download the bib entry for an article.
  2. Download a bib entry from one journal of your interest.
  3. Merge these two files into one.
  4. Cite these two references in your draft.
  • Citation style
  • Citation: [@entry].

6 Further readings

7 Exercises

  1. Convert this document into a prettydoc document. What themes can you use for it?
  2. Improve the R Markdown slides with appropriate forms, including statements, tables, and graphs. If necessary, use xaringan.
  3. Group work: The ENV221 book.
  • Each group claims one week’s teaching document.
  • Create a bookdown project. Convert each teaching document into a book chapter. Take care of the cross references for equations, tables, and graphs.
  • Merge all the chapters into one.