R Markdown and automatic reporting

Raphael Rehms

Automatic reporting

Standard way

  1. Run analysis code - Generate graphics - Generate tables - Other quantities (single numbers or summary statistics)

  2. Save it

  3. Import it into you report script

  4. Something changed due to reasons…

    • data changed
    • forgot something
    • style changes
    • … … and repeat 1-3

Pros / Cons

Pros

  • No need to learn new tools
  • Post processing of graphics possible

Cons

  • Time consuming
  • Error prone
  • Reproducibility questionable

R Markdown

Dynamic reporting with R Markdown

  • Combine report and analysis in one document:

    • Write report in an .Rmd file
    • Integrate code to produce results in the same document
    • Generate report from the document

  • R Markdown combines Markdown (.md) with the R code

  • Markdown is a simple markup language

  • Done by the R package knitr: Runs R code and integrates the result automatically in a markdown document

How to do?

  1. Open new RMarkdown document
  2. Write content
  3. Render the document

Rmd files contain 3 parts:

  • YAML header
  • Markdown text
  • R chunks

YAML header

  • The header defines ‘global options’ such as
    • Title
    • Author
    • Date
    • Output format (e.g. pdf_document, html_document, word_document)
    • Style

Markdown Text

  • Write text using markdown syntax:
# Header 1
## Header 2
### Header 3

Note the space after #!

Backticks for `Code`
*Text in italics*
**Text in bold**
***Text in italics and bold***

Special symbols require a \ in front, e.g. \# for #

Math can be included using $ inline or $$ for math block.

  • e.g. $\alpha$ will get \(\alpha\)

  • e.g. the following

$$
 \sum_{i = 1}^N X_i
$$

will get \[ \sum_{i = 1}^N X_i \]

Code chunks

  • Code chunks contain the code, that we want to use in the markdown document.
  • Either use the button, Crtl+Alt+I or write it by wrapping code using bakcticks
  • Code chunks look like this:

```{r}

R code here

```

  • You can add further arguments in the code chunk header or a name, e.g.

```{r Figure 1, eval=TRUE, echo=FALSE}

R code here

```

  • We can inline code evaluation using only one backtick and r like this:

` r 1 + 1 ` will just evaluated to 2


Look at the cheat sheets on the web, e.g.

  • this for general markdown or

  • this for R Markdown

Excercise 4 Task 1 and 2

R Markdown and automatic reporting