R Markdown

Prof. Dr. Mirco Schoenfeld

data reports

Data reports. What’s that again?


(Munroe 2021)

  • Cites other papers / journal articels / textbooks / data reports
  • Presents experimental results / calculations
  • Illustrates scenarios using drawings
  • References items in the text
  • Contains graphs / shows data

Two models of work

Two models of work.

  1. Office Model

  1. Engineering Model

https://properdiscord.com/2012/09/13/never-use-the-word-final-in-a-filename/
https://rmarkdown.rstudio.com/authoring_quick_tour.html

The difference between those models

  1. Office Model

  1. Engineering Model

The Office Model

  1. Office Model

Center of your project: Word file

  • Changes are tracked inside that file
  • Citation & Reference managers plug into Word
  • Output of data analysis is pasted into the file
  • Often, the word file is the output

The Engineering Model

Center of your project: repository

  • Changes are tracked outside of files
  • Data analysis is kept in code
  • Code produces output reproducibly
  • Citation & references in separate files
  • Final output is assembled
  1. Engineering Model

draw the owl

R Markdown

Getting Started.

https://rmarkdown.rstudio.com/articles_intro.html (Grolemund 2014)

https://daringfireball.net/projects/markdown/basics (Gruber 2004)

Basic Document

Create a basic document with the following content

---
output:
  pdf_document: default
  html_document: default
---

# Say Hello to markdown

Markdown is an **easy to use** format for writing reports.
It resembles what you naturally write every time you compose an email. In fact, you may have already used markdown *without realizing it*. These websites all rely on markdown formatting

## Subheading

Fantastic!

* [Github](www.github.com)
* [StackOverflow](www.stackoverflow.com)
* [Reddit](www.reddit.com)
* and surely others do as well!

# Chapter Two Starts Here

Let me cite some clever person:

> Dorothy followed her through many of the beautiful rooms in her castle.

Document Metadata

Now, adjust the header of the file:

---
title: "Hello World in Markdown"
author: "Mirco"
date: "24. April 2024"
---

# Say Hello to markdown

Markdown is an **easy to use** format for writing reports.
[...]

Combined data analyses

Now, for the best part, add this to the end of your document:

## What is cool about R Markdown

It is easy to show what you did by including code and output of code. The max speed of a car in our database is `r max(cars)`mp/h. We have `r nrow(cars)` cars in our dataset.

```{r}
summary(cars)
```

You can also embed plots, for example:

```{r, echo=FALSE}
plot(cars)
```

With references

To use references, adjust the header and end of your document:

---
title: "Hello World in Markdown"
author: "Mirco"
date: "27. October 2022"
output:
  pdf_document: default
  html_document:
    df_print: paged
csl: apa.csl
bibliography: references.bib
---

[...]

# References

With references

…create a references.bib file…

@book{2020-healy-plain_text,
  author ={Healy, Kieran},
  title= {{The Plain Person’s Guide to Plain Text Social Science}},
  url={https://plain-text.co/},
  publisher={The Internet},
  year={2019}
}

…and download the apa.csl here (or look for more )

It’s your turn

  1. Download the dataset to the folder of your R Markdown file
    Don’t forget to set the working directory
  2. Within the R Markdown file, load the dataset using read.csv
    The file is tab-separated
  3. Visualize the data using the plot-function
    temperature on x-axis, pressure on y-axis

And please take a look at the next slide

It’s your turn - a tip

In case you face issues installing rmarkdown package on Windows

You need to install RTools: https://cran.rstudio.com/bin/windows/Rtools/

And please check

download.file("https://cran.rstudio.com/src/contrib/PACKAGES", "text.txt")

if that results in an error:

In download.file(“https://cran.rstudio.com/src/contrib/PACKAGES”, : URL ‘https://cran.rstudio.com/src/contrib/PACKAGES’: Status war ‘SSL connect error’

Then this helps:

options("download.file.method"="wininet")

and after that install rmarkdown package

Further Reading

Advanced Usage:

https://plain-text.co/pull-it-together.html#pull-it-together (Healy 2019)

References

Grolemund, Garrett. 2014. Introduction to R Markdown. R Studio. https://rmarkdown.rstudio.com/articles_intro.html.
Gruber, John. 2004. Markdown. The Internet. https://daringfireball.net/projects/markdown/basics.
Healy, Kieran. 2019. The Plain Person’s Guide to Plain Text Social Science. The Internet. https://plain-text.co/.
Munroe, Randall. 2021. “Types of Scientific Papers.” https://xkcd.com/2456/.