MD RMarkdown templates

Install:

if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("mdozmorov/MDtemplate")

Use: In your RStudio session, select "File / New file / R Markdown / From Template ".

Table of content

• Code template
• Grant template
• Manuscript template
  • Writing tips
  • Figure tips
  • Reviewing tips
• Xaringan presentation template
  • Building blocks for Xaringan
• Quarto presentation
• No longer using

Code template

Example

A template with Rmd header and footer

Grant template

Example

A template with YAML header containing BibTex bibliography, reference formatting, and Word output template. Includes basic grant structure, and an R code for timeline Gantt chart.

Manuscript template

Example

Track/commit only text files (R, md, Rmd, txt, csv)! Do not commit large binary files (docx, xlsx, pptx, etc.) into GitHub repository. Every time such a file change, it changes completely and gets committed as such. This will grow your GitHub repository very fast. If needed, clean the repository using https://rtyley.github.io/bfg-repo-cleaner/

Writing tips

• Keep the central idea in mind, and make a list of points to illustrate it.

• Be critical and creative, ask any questions you may think of, develop strategies to answer them.

• Make a structured strategy to answer your questions. Think bulletpoints.

• Name your bulletpoints like newspaper headers - they should tell the story without the need to read the writeup.

• Address the following questions under each header:

  • What is the question?
  • What data/methods are used?
  • Any relevant details/results?
  • What is the answer (take home message)?

• Don't run your analyses on full datasets. Make sure your pipeline works from start to finish on a small subset of the data, then scale up.

• Read more, get inspiration from how others present results, what they discuss, which figures they show.

• As you add files, describe them in the README.md. Add brief description of each file.

• Savage, Van, and Pamela Yeh. “Tips from a Pulitzer Prizewinner,” - Tips for writing scientific papers: minimalism = clarity, make 2-3-points home message, one paragraph = one message, use short sentences, use fast-paced narrative, avoid over-elaboration, use commas and dashes appropriately, more.

• The Modern Language Association (MLA) citation and format style and other General Writing Resources from Purdue University

• Creating and publishing a scientific masterpiece - JCI Editor at Large Ushma S. Neill provides updated advice on generating a scientific manuscript with maximum impact. 40min

Figure tips

• Rules for better figures: 1) Know your audience; 2) Identify your message; 3) Adapt the figure to the support medium; 4) Captions are not optional; 5) Do not trust the defaults; 6) Use color effectively; 7) Do not mislead the reader; 8) Avoid chartjunk; 9) Message trumps beauty; 10) Get the right tool (Matplotlib, Inkskape, GIMP, others). Examples of good and bad figures.
  • Rougier, Nicolas P., Michael Droettboom, and Philip E. Bourne. “Ten Simple Rules for Better Figures.” PLoS Computational Biology 10, no. 9 (September 11, 2014): e1003833. https://doi.org/10.1371/journal.pcbi.1003833.

Reviewing tips

• Guidelines and ideas for providing objective reviews, addressing quality and impact (Box 1). Recommendations on review behavior to avoid (Box 2). https://immunox.ucsf.edu/future-immunology
  • Krummel, Matthew. “Universal Principled Review: A Community-Driven Method to Improve Peer Review,” 2019

Xaringan presentation template

A template for a Xaringan HTML presentation. Examples of columns, image/video embedding, panels, footnotes, other tweaks using XaringanExtra. Presentation example.

Building blocks for Xaringan

Xaringan by Yihui Xie is a great package to make good looking and portable presentations.

presentation.Rmd contains YAML settings and basic examples reminding how to insert an image, make two-column slide etc. Example.

Learn more about xaringan Presentations. This example is not meant to be comprehensive.

xaringan-my.css contains .large[], .small[], and .tiny[] formatting styles. xaringan-themer.css is created by xaringanthemer in the corresponding chunk in presentation.Rmd.

xaringanExtra by Garrick Aden-Buie makes the presentations even more flexible.

xaringanBuilder - An R package for building xaringan slides into multiple outputs, including html, pdf, png, gif, pptx, and mp4.

Quarto presentation

• https://quarto.org/docs/presentations/revealjs/demo/ - live demo
• https://github.com/quarto-dev/quarto-web/blob/main/docs/presentations/revealjs/demo/index.qmd - code for the demo

No longer using

Beamer presentation template. Example

A template for a PDF presentation using Beamer formatting (theme, color). Examples of slide formatting are at https://github.com/mdozmorov/beamer_template/blob/master/presentation.pdf