Communicating with R

  • All research results must be communicated at some point

  • Results are encoded in text, tables, and plots

  • Methods are described in text, and (ideally) the code itself

    • Many journals now require code to be made available upon publication

  • Providing code can make analyses more reproducible

  • Code notebooks are tools that combine code, results, and text into one place

Markup langauges & markdown

  • A markup language annotates and decorates plain text with information about its formatting and structure

  • Both machine- and human-readable

  • The same markup text might be converted into different formats, e.g. HTML or PDF

  • markdown is one such markup language

Markdown Examples

You can *emphasize* text, or **really emphasize it**.

Lists are pretty easy to read as well:

* item 1
* item 2
* item 3

You can emphasize text, or really emphasize it.

Lists are pretty easy to read as well:

  • item 1
  • item 2
  • item 3

Markdown Examples

If you need an enumerated list you can do that too:

1. item 1
2. item 2
3. item 3

If you need an enumerated list you can do that too:

  1. item 1
  2. item 2
  3. item 3

Markdown Examples

You can easily include links to web sites like
[Google](http://google.com) and images:
![kitty](https://upload.wikimedia.org/wikipedia/commons/b/bc/
  Juvenile_Ragdoll.jpg)
You can easily include links to web sites like Google and images:

Markdown Tables

+------+------+-----+-------+
| some | data | and | stuff |
+======+======+=====+=======+
|   A  |   1  |  2  |   3   |
+------+------+-----+-------+
|   B  |   4  |  5  |   6   |
+------+------+-----+-------+
some data and stuff
A 1 2 3
B 4 5 6

RMarkdown

  • RMarkdown is an extension of markdown that works in R
  • Can include code blocks in R in between markdown formatted text that execute
  • Files with RMarkdown are called RMarkdown notebooks
  • RMarkdown files typically end with .Rmd
  • RStudio has full RMarkdown integration to make writing RMarkdown notebooks very easy

R code blocks in RMarkdown

  • Lines starting with ```{r} define a special code block

  • Example:

    
``` r
a <- 1
```

  • R code in the block will be executed

  • Code output placed below the block in the report

  • RStudio shows you the output of the notebook within its interface

RMarkdown in RStudio

R code block output

knitr

  • The knitr R package turns RMarkdown into a report
  • The process is called “knitting”
  • Same report can be knitted into many different formats
    • HTML
    • PDF
    • Microsoft Word
    • Slides (like these ones)

bookdown

  • Another R package that processed RMarkdown documents is bookdown
  • Designed to write books using RMarkdown
  • This book you are reading was written in RMarkdown and generated using bookdown!