Why this workshop?

• In the social sciences few attention to what tools to use (and why they make sense)

• Increasing need for/in openness & transparancy

  • from journals, universities and governments
  • increase in cooperation (over wider distances)
  • access to your own files
  • make yourself more visible

Goals of this workshop

• To make you familiar with some concepts and tools, being aware of the facts that
  • there is no general, optimal, set of workflow tools
  • investment is very, very costly (in time that is)

• However, being a practical workshop we do

  • work with a specific set of tools to
  • touch upon the concepts of markup languages, versioning and opening up.

• Specifically, we use

  • Markdown to format a piece of text into a paper,
  • RStudio as a general editor,
  • Git to keep track of what we have done,
  • GitHub to make our material public and share as a website.

How we will do it in this workshop

• Every session start with some introductionary slides

• Then some hands-on and in-class assignments

• All materials can be found on thomasdegraaff.nl/ERSA-WooW/

Related work

• Inspired by Kieran Healey’s (associate professor in sociology) work: Choosing your Workflow Applications

• Some on-line courses for reproducible research:
  • Datascience course: https://www.coursera.org/
  • Tools for Reproducible Research http://kbroman.org/Tools4RR/
• Shameless self-promotion:
  • With Daniel Arribel-Bel: WooW-II workshop: https://github.com/darribas/WooWii;
  • with Daniel Arribas-Bel: REGION resource
  • with Daniel Arribas-Bel and Serge Rey: Regional Research Frontiers forthcoming book chapter

Open?

• Workflow:
  • Progression of steps (tasks, events, interactions) that comprise a work process, involve two or more persons, and create or add value to the organization’s activities (BusinessDictionary)
• Open workflow:
  • One that enhances transparency, collaboration and reproducibility

Ideal research cycle

Research cycle in theory

Research cycle in practice

Research cycle in practice

Why bother about a (open) workflow or tools?

• Good scientific practice: document how you have achieved your results

• A good reproducible workflow ensures

  • reproducibility (duh….);
  • transparency;
  • modularity;
  • portability (across systems and users);
  • efficiency;
  • self-sanity.

When should I adopt a (open) reproducible workflow?

• The sooner the better
• But think twice about which one (switching is costly)
• Start one step at a time

A journey of a thousand miles begins with a single step

Lao-tzu

In general

In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus (Michael Crichton)

In computation science:

The data and code used to make a finding are available and they are sufficient for an independent researcher to recreate the finding (Peng, 2011)

• Literature programming (Donald E. Knuth, 1984):

  • weaving of code, documentation and output (articles, presentations, websites)

In the social sciences?

• Complete reproducibility often not feasible
  • qualitative research
  • proprietary data (?)
• but you can come a long way, especially with
  • theoretical work
  • quantitative (e.g., statistical or simulation) work
• Goal should be more to make your research as reproducible as possible

Code, documentation and output

1. Synonyms

2. All based on text files

3. Encompasses almost anything, e.g.:
   • data itself
   • set of commands for data cleaning and statistical analysis
   • database with references
   • transcript of interviews
   • text for aticles, presentations or websites

4. Only output is displayed/interpreted differently (e.g., in a browser or pdf viewer)

Tools for reproducibility

• Markup lanaguages
  • Markdown

• Versioning system (Git)

• Online repository (GitHub)

• Terminal tools (diff, Pandoc)
  • RStudio
  • GitHub DeskTop

Only implicitly we make use of LaTeX, diff, HTML and Pandoc (all under the hood of RStudio)

Schedule

1. Introduction to reproducibility and open science workflow principles (30 mins.)
   • Install GitHub account and GitHub Desktop
2. Markdown language (45 mins.)
   • Draft an outline of a paper with Markdown
3. Principles behind Git and workflow examples (45 mins.)
   • Version draft paper with Git
4. Publication of your material on the open repository GitHub (45. mins).
   • Push paper to Github
   • Add README file with Markdown
   • Publish paper on Github pages

Get Github account and Install GitHub Desktop

1. Go to https://github.com/join and create account (the name is what people see so think twice)
2. Go to https://desktop.github.com/ and install GitHub Desktop (already done on these computers)
3. Find the repository ERSA-WooW and copy it (fork)
4. In GitHub Desktop go to options and add your account.
5. click the + and clone ERSA-WooW.