3 min read

RMarkdown

2017/03/21

Before you start, install rmarkdown package and download “R Markdown Cheat Sheet” and “R Markdown Reference Guide” from

https://www.rstudio.com/resources/cheatsheets/

There exist many good introductions to RMarkdown:

Try to understand enough of RMarkdown to get through Challenge 1.

markdown

Challenge 1:

Create a new R Markdown file (File -> New File -> Document). First run “Knit” document to see HTML output. Then find or add the following formatting marks:

  • bold, italics, code-type
  • headers: title, main section, sub-section, sub-sub-section (its the same symbol, just repeated multiple times)
  • link to the page
  • figure caption

options

If you look at your .Rmd file from Challenge 1, you might realized a strange thing. For the first chunk (summary(cars)) R code is a part of HTML report while for the second chunk (plot(pressure)) we see only output but not R code itself. This is controlled by chunk options:

  • Use echo=FALSE to avoid having the code itself shown.
  • Use results="hide" to avoid having any results printed.
  • Use eval=FALSE to have the code shown but not evaluated.
  • Use warning=FALSE and message=FALSE to hide any warnings or messages produced.
  • Use fig.height and fig.width to control the size of the figures produced (in inches).

If you forget a syntax you can always click on a little wheel in the chunk’s top right corner and select it in a menu. You can also run a chunk in a console after clicking on the green arrow.

If you want to set default options for all chunks, you can use knitr::opts_chunk$set function.

Challenge 2

Add a new chunk with ggplot2 figure to your Rmd file. Use chunk options to control the size of a figure and to hide the code.

formats

RMarkdown processing consist of two steps: * knitr package is used to run all the chunks and replace them by their output, the result is markdown (.md) file * some other software (like pandoc) process markdown file into final format

Challenge 3

Look at the header of your document where the output format is specified. Change it from output: html_document to output: word_document or output: pdf_document to produce MS Word or PDF document.

summary

There are many other ways to use RMarkdown:

  • presentation slides with xaringan package
  • a blog with blogdown package - like this page
  • a book with bookdown package - like R for Data Science
  • a reproducible workflow with workflowr package

Once something is written in markdown format, it is quite easy to switch from HTML to PDF to slides to workflowr or blog.

Also with RMarkdown it is easier to make your analysis reproducible:

http://kbroman.org/steps2rr/