10 RMarkdown & Knitr

10.1 Knitr

Knitr is a feature in RStudio that will turn your R programme into a HTML (or PDF/Word) document.

You need to use RMarkdown, and write your R code in ‘chunks’. You can include regular markdown text, and also html, javascript or python.

Knitr will evaulate all the code and embed any tables/charts/maps into the output.

10.2 YAML

At the top of all RMarkdown documents there is some YAML code:

---
title: "Untitled"
output: html_document
---

YAML includes information that tells Knitr what type of document to create. In the example above it wil be a HTML document.

However it cann also be used to add a table of contents, or to allow users to input cutom paraemters.

Adding a table of contents

---
title: "Untitled"
output: html_document
  toc: TRUE
---

Nb. That the contents is automatically generated based on any RMarkdown header tags ‘#’ that you have used.

Adding parameters Parameters can be added after the params: option. They must have a label and a value. By defaut the parameter will be a textbox.

---
title: "Untitled"
output: html_document
params:
  parametername1:
    label: "Display label"
    value: "Default value"
---

Different types of parameter input are allowed, such as check boxes and dropdown lists.

---
title: "Untitled"
output: html_document
params:
  mycheckboxparam:
    label: "Display label"
    value: TRUE
  mydropdownparam:
    label: "Display label"
    value: apples
    input: select
    choices: [apples,oranges,bananas]
---

You can refer to the parameter values in the rest of the your code using the form params%parametername1

To use these parameters the Rmarkdown document must be Knitted using ‘Knit with parameters…’

10.3 Modular coding

If your R code is written in modules, then you can call them using the source() function, eg:

source('module1.r')
source('module2.r')