Recap

• Ideally everything is based on text
• Markdown is a very easy markup language
• Pandoc can combines languages and convert to pdf and HTML
• This means that your writings (articles & presentation) can be converted simultaneously to:
  • pdf for dead trees
  • HTML to be published on your website

Goal

• to make your research as reproducable as possible and open
  • so that others can actually reproduce it!
• This means publishing your paper together with the rest of your analysis, including
  • code
  • data (if infeasible—descriptives)
  • figures

Why again?

• Actually makes you more visible
• Easier to collaborate
• Enforces your to work ‘tidy’
• For the ‘greater good’
  • faster dissemination
  • ultimately reduces errors (e.g., Piketty, Reinhart and Rogoff)

Final part of this workshop

1. Combining code and text

2. Creating presentations

3. Online publishing

4. Bring it all together

Combining code and text

• RStudio uses the package knitr

• Actually knitting in chunks of code within text.

• example

Discussion: code within text or as separate files?

Knitr options:

• Typically:

{```}{r, echo=FALSE, results='hide', 
        warning=TRUE, warning=TRUE, message=TRUE}
rnorm(10)
{```}

• Or:

{```}{r, echo=FALSE}
source("./file.R")
{```}

Slides

• pdf — good for printing (handouts)

• HTML
  • enables dynamic presentations
  • enables incorporating slides in websites/blogs, etc.

Markdown, pandoc and a bit of LaTeX

• In RStudio remarkably easy to incorporate

• If you have ever made beamer slides this is a huge time saver

• Makes you flexible.

• And incorporates code!

• So, with one make file presentations are updated as well!

Github’s repositories

• git is versioning application, but:
  • research is not backed up
  • and not yet open
• That is why we use Github :
  • requires inlogname + psswrd
  • Creates your own repository space (just like LinkedIn or, worse, Facebook!)
    • For all materials (extends .txt files)
    • Allows for corporation (with known and unknowns)
    • And finally allows to create your own website

How does Github work?

• For complete packages (it is not a file server)

• It is open
  • Everyone can download your stuff/you can download everything (datestamps!)
  • Which also means that everyone can contribute to your code (actually push & pull request)
  • Collaboration is a breeze (using the automatic diff commands)
  • Very intuitive gui’s

How does Github work? (cnt.)

• So you push to a repository

• And you pull from a repository

• If you like something you can fork a repository (on Github) > Forking a repository allows you to freely experiment with changes without affecting the original project.

• If you would just like a copy of a repository on a computer you should use clone

And finally, websites

• Using Github pages (gh-pages); you get something like: darribas.github.io/WooWii/

• Useful for blogs

• Showcase of projects http://darribas.org/bits/

Other publication channels

• for Git other open repositories such as Bitbucket

• for R:
  • RPubs
  • create a package from your paper (and publish on CRAN)
  • iPython notebook viewer

Assignment 5

• go to /WooWii/Paper/Assignment5/

• Incorporate source files using knitr

• publish on your own github repository

• if time permits and with OsX, create a makefile structure to create with one command
  • pdf output
  • doc output
  • html output