Recap

Our main goal:

To make our research as reproducable and visible as possible

This entails:

1. Sharing of code
2. Sharing of data (if possible and not proprietary nor privacy sensitive)
3. Sharing of output (presentation, article, website)

The power of plain text

1. Ubiquitous
2. Usually small in size
3. Portable across platforms (and versions)
   • it will not be obsolete soon
   • everyone can read it everywhere
4. It is scriptable (both as input as output)
   • code is almost always in text format
   • usually data is in text format as well
   • but underlying format for output (presentation, website, tables, articles, books) can be text as well

Manipulation of text

• Most output is based on simple text file; applications only change appearance, such as:
  • browsers
  • pdf
• How to change appearance require markup-languages
  • HTML
  • LaTeX
  • Markdown

Why markdown?

1. Easy to learn http://daringfireball.net/projects/markdown/

2. Much less notation than LaTeX. Originally,

   • LaTeX is for paper (aka dead trees)
   • Markdown is for HTML (blogs, wikipedia and so)
   • but sneakily uses some LaTeX when needed
3. Focus on text

4. Nowadays:

   • “easily” change it in html or pdf (via LaTeX)—even in Word’s .docx if needed (but error prone)
   • can be extended with code (verbatim) or—even better—its results

Small diversion

Question 1: Why and when do we make use of pdf’s and not html?

Question 2: Is one always better than the other?

Language syntax

Emphasis:

*italic* **bold**
_italic_ __bold__

Headers:

# Header 1
## Header 2
### Header 3

Language syntax (cont.)

Unordened lists

* Item 1
* Item 2
    + Item 2a
    + Item 2b

Ordered List

1. Item 1
2. Item 2
3. Item 3
    + Item 3a
    + Item 3b

Language syntax (cont.)

Links: Cheatsheet

[Cheatsheet](http://assemble.io/docs/Cheatsheet-Markdown.html)

Images:

![alt text](http://example.com/logo.png)
![alt text](figures/img.png)

footnotes:

As it is well known¹

As it is well known[^fn1]
[^fn1]: You know nothing, John Snow

Language syntax (cont.)

Code blocks:

    ```python
    s = "Python syntax highlighting"
    print s
    ```
    

which renders as:

s = "Python syntax highlighting"
print s

Language syntax (cont.)

To embed mathematics ‘just’ use LaTeX (see here for list of symbols and note that LaTeX should be installed on your computer):

$$e=mc^2$$

which surprisingly looks as excel type of formulae and renders as:

\[e=mc^2\]

Language syntax (cont.)

Inline equations just require $ $, e.g.:

In economics it is well known that: 
$\frac{d x}{d y} = -\frac{
\partial u(x,y)/ \partial y} {
\partial u(x,y)/ \partial x}$.

which renders as

In economics it is well known that: \(\frac{d x}{d y} = -\frac{ \partial u(x,y)/ \partial y} { \partial u(x,y)/ \partial x}\).

The swiss knife of formats

So how do we glue everything together and produce wonderful htmls and pdfs out of thin air? With pandoc

• Pandoc can convert from (not extensive):

  • Markdown (whoohoo), LaTeX, HTML, DocBook, Org-mode, and … Words docx (sort off)

• To (and here we go…)

  • HTML formats (including those very cool and nerdy HTML(5) slides)
  • via Latex to pdf
  • Word (but support somewhat limited) and OpenOffice formats
  • various markup formats
  • and much more

The assignment

• if not already done do:

  • clone thdegraaff/ERSA-WooW and save it locally

• go to the folder ./Assignments/

• Open Assignment1.md in RStudio

• and transform Assignment1.md as much as possible in RStudio:

  • This means adding Markdown tags to the basic text
  • The file HowToWriteAShinyPaperLimited provides a LaTeX example how the format sort of should be.

• Save it with the same name.