rbtl - Research Beyond the Lab

# rbtl - Research Beyond the Lab
## Literate Programming with R Markdown
### Lars Schöbitz
### 2022-04-28

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# Today

1. Homework Assignment 3 - How to get solutions?
1. R Markdown 
1. Homework Assignment 4

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# Remember?

## `git clone`

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# Remember?

## `git commit`

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# Remember?

## `git push`
 
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# Collaborate!

## `git clone`

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# Track work

## `git commit`

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# Update

## `git push`

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# New!

## `git ???`

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# Get changes

## `git pull`

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# Commit history

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## R markdown

### On the input side...

- Write text in markdown
- Insert code using R
- Write "metadata" with YAML
- Insert equation with LaTeX
]

### On the output side...

- Output to HTML
- Output to PDF
- Output to Word
- Many other variations too
]

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# Word documents are complicated

- A .docx file is a compressed folder with lots of files
- A .docx file is proprietary file format 
- Your text is buried in with a lot of formatting information

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# HTML documents are complicated

- Looks simple because I removed most formatting
- Still unpleasant to look at

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# What do we want?

- Something that... you can write in **plain text**
- Something that... is **human readable** 
- Something that... allows **formatting**
- Something that... can **build** to something pretty

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# markdown file format

> A markup language with a simple syntax intended as a replacement for HTML - [Definition](https://glosario.carpentries.org/en/#markdown)

- Is a **markup language** - [Definition](https://glosario.carpentries.org/en/#markup_language)
- Is an **open format** - [Defintion](http://opendatahandbook.org/glossary/en/terms/open-format/)
- Is **non proprietary** - [Definition](http://opendatahandbook.org/glossary/en/terms/proprietary/)

???

#### markup language

- A set of rules for annotating text to define its meaning or how it should be displayed

#### open format

- file format with no restrictions, monetary or otherwise
- can be fully processed with at least one free/libre/open-source software tool. 
- the structure of an open format is set out in agreed standards, overseen and published by a non-commercial expert body
- Patents are a common source of restrictions that make a format proprietary

#### proprietary

- A proprietary file format is one that a company owns and controls. 
- Data in this format may need proprietary software to be read reliably
- Proprietary software usually reads and saves data in its own proprietary format

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Welcome to my **awesome** class. You will learn 
all kinds of useful things about R markdown.

## Why should you care?

- Markdown is simple and reproducible
- You can make it pretty if you want to
- The R Markdown variant lets you add R code

## Where can you find these slides?

https://rbtl-fs22.github.io/website/posts/week4/

```
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.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# Introduction

Welcome to my **awesome** class. You will learn 
all kinds of useful things about R markdown.

## Why should you care?

- Markdown is simple and reproducible
- You can make it pretty if you want to
- The R Markdown variant lets you add R code

## Where can you find these slides?

https://rbtl-fs22.github.io/website/posts/week3/

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## Emphasising text

--
.pull-left[

### What you type...

```
this is *italics*

this is **bold**

this is ***bold italics***
```
]
--
.pull-right[

### What you get...

this is *italics*

this is **bold**

this is ***bold italics***
]

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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## Creating lists

--
.pull-left[
### What you type...
```
- unnumbered lists
- look like this

1. numbered lists
2. look like this
```
]
--
.pull-right[
### What you get...

- unnumbered lists
- look like this

1. numbered lists
2. look like this
]

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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## Creating headings

--
.pull-left[

### What you type...

```
# Level 1 heading
## Level 2 heading
### Level 3 heading

```
]
--
.pull-right[

### What you get...

# Level 1 heading
## Level 2 heading
### Level 3 heading
]

.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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# R markdown

- Something that... lets you write text in **markdown**
- Something that... lets you include **R code** (e.g. for data vis)
- Something that... can **build** to HTML, PDF, Word, etc
 
.footnote[Slide taken from: [Danielle Navarro - R markdown](https://slides.djnavarro.net/starting-rmarkdown/#1)]

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background-image: url(https://bookdown.org/yihui/rmarkdown-cookbook/images/workflow.png)
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.footnote[Image from: [R Markdown Cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/rmarkdown-process.html)]

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# Homework Assignment 4 - Learning Objectives

These learning objectives are related to the assignment for this week.

- Learners can explain the difference between the markdown (.md) and R Markdown (.Rmd) file format
- Learners can paraphrase how a file written in a markup language like markdown (.md) differs from a file written in a proprietary file format like DOCX
- Learners can identify four components of an R markdown file (YAML, code chunk, R code, markdown)

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# Homework Assignment 4 - Group work submission

- Due on **22nd March**

## Exercise 2: Each ~~group~~ person will

1. Add the research questions that you and/or your group have worked on.

2. Write up the research design you are planning to use for your data collection.

3. Submit their sample population:

- Bins: (1) Number; (2) Location, (3) Frequency of sampling
  - Human population, for example random, over 60, family, cyclist, etc.

4. Write up the variables that are needed, together with the respective questions and possible response values.

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# Bin location?

You can download a CSV with data on all bins from:

- https://www.ogd.stadt-zuerich.ch/geoportal_download/71dc10de-a5e2-11ec-94cb-005056b0ce82.zip (**valid until 22nd March**)
- https://www.stadt-zuerich.ch/geodaten/download/Abfallgefaesse (**Stadt Zürich Open Data, in German**)

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# Thanks! 🌻

Slides created via the R packages:

[**xaringan**](https://github.com/yihui/xaringan)<br>
[gadenbuie/xaringanthemer](https://github.com/gadenbuie/xaringanthemer)

The chakra comes from [remark.js](https://remarkjs.com), [**knitr**](http://yihui.name/knitr), and [R Markdown](https://rmarkdown.rstudio.com).

Access slides as [PDF on GitHub](https://rbtl-fs22.github.io/website/slides/pt2-d04-rmarkdown/pt2-d04-rmarkdown.pdf)

All material is licensed under [Creative Commons Attribution Share Alike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/).