Econometrics & Programming with R - Seesion 4.1 - Rmarkdown

Overview

• R Markdown provides an authoring framework for data science.

• You can use a single R Markdown file to both:

  • save and execute code
  • generate high quality reports that can be shared with an audience

• R Markdown documents are fully reproducible and support dozens of static and dynamic output formats.

• See the introductory video

Installation

• You can install the R Markdown package from CRAN with:

install.packages("rmarkdown")

• You may also find the following resources helpful:
  • The R Markdown Cheatsheet
  • The R Markdown Reference Guide

How It Works

• A plain text file that has the extension .Rmd

• Notice that the file contains three types of content:

  • An (optional) YAML header surrounded by “- - -”

---
title:...
author:...
date:...
output:...
---

How It Works

• A plain text file that has the extension .Rmd

• Notice that the file contains three types of content:

  • R code chunks surrounded by ```s
  • Text mixed with simple text formatting

• When you open the file in the RStudio IDE, it becomes a notebook interface for R.

• You can run each code chunk by clicking the run button

Rendering output

• To generate a report from the file run the render command within a chunk:

library(rmarkdown)
rmarkdown::render("Lecture_4.1_Rmarkdown.Rmd", output_format = "word_document")

• Or use the “Knit” button in the RStudio integrated development environment (IDE) to render the file and preview the output with a single click or keyboard shortcut (⇧⌘K).

Picture 1

Rendering output

• We can set a default output within the menue of the “knit” button

Picture 2

How it works

Picture 3

• When you run render, R Markdown feeds the .Rmd file to knitr which executes all of the code chunks and creates a new markdown (.md) document which includes the code and it’s output.
• The markdown file generated by knitr is then processed by pandoc ⧉ which is responsible for creating the finished format.
• The new file can be a finished web page, PDF, MS Word, document, slide show, notebook, handout, book, dashboard, package vignette,or other format.

Code Chunks

• You can quickly insert chunks like these into your file with
  • the keyboard shortcut Ctrl + Alt + I (OS X: Cmd + Option + I)
  • the Add Chunk command in the editor toolbar

Picture 4

Chunk Options

• Chunk output can be customized with knitr options or, arguments set in the {} of a chunk heade. For instance:

{r include = FALSE}

Include = FALSE prevents code and results from appearing in the finished file. R Markdown still runs the code in the chunk, and the results can be used by other chunks.

{r echo = FALSE}

echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.

Chunk Options

{r message = FALSE }

message = FALSE prevents messages that are generated by code from appearing in the finished file.

{r warning = FALSE}

warning = FALSE prevents warnings that are generated by code from appearing in the finished.

{r fig.cap = "..."}

fig.cap = “…” adds a caption to graphical results.

Chunk Options

• Example

{r, out.width = "200px", fig.cap = "Example"}
image(volcano, col = viridis(200))

image(volcano, col = viridis(200))

Example

• For more options see the following link

Chunk Global Options

• To set global options that apply to every chunk in your file, call knitr::opts_chunk$set() in a code chunk.

• For instance:

{r}
knitr::opts_chunk$set(echo = TRUE)

Dashboards

• Dashboards are a useful way to communicate large amounts of information visually and quickly.

• We will create one with the flexdashboard::flex_dashboard output format.

• Flexdashboard makes it easy to organize your content into a visual layout:

  • Each Level 1 Header (#) begins a new page in the dashboard.
  • Each Level 2 Header (##) begins a new column.
  • Each Level 3 Header (###) begins a new box.

Dashboards

• We can further modify elements with attributes, as in the {.sidebar} above.
• Flexdashboard also provides simple tools for creating tabsets, value boxes, and gauges. Learn more about flexdashboard at flexdashboard: Easy interactive dashboards for R

Dashboards example

Picture 4

Interactive Documents

• R Markdown documents are a perfect platform for interactive content. To make your documents interactive, add:
  • Interactive JavaScript visualizations based on htmlwidgets
  • Reactive components made with Shiny