Chapter 50 Rmarkdown tutorial

Author: Shaofeng Wu, Mingrui Liu

50.1 1. Overview

R Markdown provides a tidy framework for data science. A markdown file can normally help us:
- save and execute code that you wrote
- 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.
This link provide a quick tour of what’s possible with R markdown.-links

50.1.1 1.1 What is R Markdown?

  • Rmd files
    · An R Markdown(.Rmd) file is a record of your project. It contains the code that your audience needs to reproduce your work as well as all the scripts that your audience can understand what you did.
  • Reproducible Research
    · You can use Knit to rerun the code in an R Markdown file to reproduce your work and export the results to be a well-formatted report.
  • Dynamic Documents
    · There are a lot of ways to export your report. The formats include html, pdf, MS Word, or RTF documents; html or pdf based slides, Notebooks, and more.

50.1.2 1.2 Workflow

  1. Open a new .Rmd file at File ▶ New File ▶ R Markdown.
  2. Write document by editing template
  3. Knit document to create report; use knit button or render() to knit
  4. Preview Output in IDE window
  5. Publish (optional) to web server
  6. Examine build log in R Markdown console
  7. Use output file that is saved along side .Rmd Caption

50.2 2. Getting started

50.2.1 2.1. Install the package

You can use the following command to install the required library.

50.2.2 2.2. Open file

You can create a new file or open existed from the directory that you choose.

50.2.3 2.3. output format

The Rmarkdown can render any Rmd file into a format that Rmarkdown supports. For example, the code below renders OutputExample.Rmd to a Microsoft Word document.

Following is a table of all the formats that you can choose: Output value table

output value creates
html_document html
pdf_document pdf (requires Tex )
word_document Microsof Word (.docx)
odt_document OpenDocument Text
rtf_document Rich Text Format
md_document Markdown
github_document Github compatible markdown
ioslides_presentation ioslides HTML slides
slidy_presentation slidy HTML slides
beamer_presentation Beamer pdf slides (requires Tex)

You can choose to render to the format that you want by clicking the dropdown menu beside the knit button: Caption

50.3 3. Markdown syntax

Rmarkdown has lots of fancy syntax so that you can produce an ordered and beautiful document.
We will give the syntax here that we regularly use a lot.

  • plain text
    plain text

  • italics and bold
*italics* and **bold**

italics and bold

  • list
* unordered list  
   + sub-item 1  
   + sub-item 2  
   - sub-sub-item 1
  • unordered list
    • sub-item 1
    • sub-item 2
    • sub-sub-item 1
1. ordered list
2. item 2  
 i) sub-item 1  
    A. sub-sub-item 1
  1. ordered list
  2. item 2
  1. sub-item 1
    A. sub-sub-item 1
  • headers
# Header1 {#anchor}
## Header 2 {#css_id}
### Header 3 {.css_class}
#### Header 4
##### Header 5
###### Header 6
Caption

Caption

  • hyperlink
<http://www.rstudio.com>
[link](www.rstudio.com)
Jump to [Header 1](#anchor)

http://www.rstudio.com link Jump to Header 1

  • table
| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
| 12    | 12   | 12      | 12     |
| 123   | 123  | 123     | 123    |
| 1     | 1    | 1       | 1      |
Right Left Default Center
12 12 12 12
123 123 123 123
1 1 1 1
  • equation
$$E = mc^{2}$$

\[E = mc^{2}\]

50.4 4. Embeding code

50.4.1 4.1. Inline code

You can surround code with back ticks and r. R will replace inline code with its results.

For example:

The output is:

one plus one equals 2

50.4.2 4.2. Code chunks

In this way, ou need to start a chunk with ``` {r} and end a chunk with ```

For example:

## [1] "Hello, world!"

50.4.3 4.3. Display options

There are also a lot of options to display your codes and results.

For example, you can choose eval as TRUE or False in the output to decide whether to evaluate the code and include its results.

Here is the difference between the two options:

With eval = TRUE:

## [1] "Hi there!"

With eval = FALSE:

Here is a table that includes the options that we normally use:

option default effect
eval TRUE Whether to evaluate the code and include its results
echo TRUE Whether to display code along with its results
warning TRUE Whether to display warnings
error FALSE Whether to display errors
message TRUE Whether to display messages
tidy FALSE Whether to reformat code in a tidy way when displaying it
cache FALSE Whether to cache results for future renders
comment “##” Comment character to preface results with

50.5 5. Rendering

  • first way

    You can run rmarkdown::render("<file path>") in the console.

  • second way

    You can click the Knit button in the top pane and choose the output format that you want.