markdown

markdown is a lightweight markup language with plain text formatting syntax. Its design allows it to be converted to many output formats, but the original tool by the same name only supports HTML.

Rmarkdown

Extend the markdown concept to run R code.

Full tutorial at https://rmarkdown.rstudio.com/authoring_quick_tour.html

Render

To render the Rmarkdown file to HTML or PDF, you can use the knit button or

rmarkdown::render("input.Rmd")

Using parameters

Parameters in the header of the document define format of the output.

---
title: "Sample Document"
output:
  html_document:
    toc: true
    theme: united
---

or to define variables used in the file at some point.

To render the Rmarkdown file to HTML or PDF with different parameters using the rmarkdown package:

rmarkdown::render("input.Rmd", params = list(filenames="otherfile.txt"))

Example

Download this material from github:

https://github.com/pilm-bioinformatics/pilmbc104-best-of-r/archive/master.zip

Extract the content, you should have a folder with this name: pilmbc104-best-of-r-master.

Double click on pilmbc104.Rproj.

Open tidyverse.Rmd and click knit.

Then go to the Console and type rmarkdown::render("ggplot2.Rmd").

You should see two HTML files now.