1. Transparency and reproducibility
   1. Markdown for reproducibility
   2. Git for version control
2. Outreach
   1. Markdown + Git for your academic website + CV
   2. Twitter for outreach

• Who has used Markdown previously? What for?

• Markdown, an easy way to:
  
• take notes,
  • create content for a website (HTML),
  • produce printable documents (PDFs).

• → All in one language.

• Pros
  • Easier than Word, Latex, HTML
  • Transferability of file formats
  • Integration with R via R Markdown (Rmd)

• Cons (ostensible)
  • less formating options than Word, Latex, HTML
    → But Latex and HTML can be used within Markdown
  • Submission in Word or Latex required
    → Transfer file format with one click using Pandoc

• **Bold**: Bold
• *Italic*: Italic
• ~~Striketrough~~: Strikethrough

1. first point
2. second point
   - one sub-item
   - another sub-item
3. third point

1. first point
2. second point bold
   • one sub-item
   • another sub-item
3. third point

• Sets global parameters of the document

• Markdown Guide

• Cheat Sheet

• Templates for R Markdown by Steven Miller include:

  • Academic Manuscript
  • Slides
  • Syllabus
  • Memos
  • Academic CV
  • Non academic Resume

• Use reproducR by Julia Schulte-Cloos to automatically anonymise your manuscript

• Choose a text editor; any will do. I use RStudio and VSC.

• Start by taking your notes in Markdown instead of Word,
  f or instance in this research group.

• RMarkdown: integrates R code into Markdown language.

• Knitr: changes file formats from RMarkdown to Markdown.

• Pandoc: converts between different markup languages (docx, HTML, LaTeX, and Markdown).

• Who has used Git previously? What for?

• Who has used any kind of version control previously?

• “Save early, save often”.
• Easiest version control: the back-button.
• “Track-changes” in MS Word: rudimentary form of version control.

Git is sophisticated version control:

• Single, updated version of each file.
• Record of all previous versions.
• Record of exact changes between the versions.
• Collaborators can work simultaneously.
• Documents who made changes, when and why.

• Maintain an overview
• Access previous versions

• Strengthen Collaboration
• Foster Transparency

• Create an academic CV
• Create an academic website
• → Rmd allows you to use the same document for both

• repository (repo)
• commit
• diff

• branch
• remote
• local
• commit message and tag
• gist

• repository (repo): directory of files
• commit: snapshot of directory
• diff: difference between two commits

• branch: detour from main stream without changing main stream
• remote: repo hosted online
• local: repo on your hard drive (offline)
• commit message and tag: notes assigned to commits
• gist: small repo to share one code file

• to commit
• to merge
• to fork
• to clone
• to push
• to pull

• to commit: create a commit
• to merge: merge on branch into another branch
• to fork: create a copy of someone else’s repo in your GitHub account
• to clone: create your local copy of the repo
• to push: upload changes from your local to your remote
• to pull: update local from remote

• Install and use GitHub Desktop (especially for beginners)

• 1h Introduction
• Happy Git intro for data science
• Learn Git Branching tool

• GitHub pro is free for students (Sign up for GitHub Student Developer Pack).
• GitHub Teacher Toolbox is free for course instructors.

• Oxford ReproducibiliTea
• Berkeley Initiative for Transparency in the Social Sciences

• GitHub Pages: you get a free domain to host your website on github.io.
• Your GitHub repository: is as your server.
• Markdown: .md files contains your content.
• Static site generator, for instance Jekyll or HUGO:
  takes your Markdown files and builds an HTML website.
• Choose a theme, for instance Minimal Mistakes to begin with.

→ No knowledge of web programming (HTML, CSS, JavaScript,…) required.
Disclaimer: but some bits may still be helpful later on to customise your work.

• Consist of Markdown Syntax

• Set global parameters of the document in the YAML header

• Include general information in the _config.yml file

• Allow you to adjust html and css - but you do not need to!

• Test changes locally:
• Start local site: Type bundle exec jekyll serve in the command line
• Visit local site: Open localhost:4000/yourwebfoldername/ in a web browser (e.g. localhost:4000/JekyllDemo/). Don’t forget the trailing slash!

• The vitae R package
• datadrivenvc package by Nick Strayer
• Markdown for Latex and HTML template (my CV) based on templates by Alex Albright and Steven Miller

• Who is using Twitter? What for?

1. Get information

1. Get information
2. Share your work

1. Get information
2. Share your work
3. Interact with peers

1. Get information
2. Share your work
3. Interact with peers
4. Advice for your community

1. Get information
2. Share your work
3. Interact with peers
4. Advice for your community
5. Outreach and Impact

1. Your profile is key: bio + photo + link + pinned tweet.
2. Tweet original messages. But support others too.
3. Tweet to the right time. Schedule with https://tweetdeck.twitter.com/.
4. Follow and be followed back. But do not overdo it. Unfollow who unfollows you https://who.unfollowed.me/.
5. Be aware of the Matthew effect.

1. Your profile is key: bio + photo + link + pinned tweet.
2. Tweet original messages. But support others too.
3. Tweet to the right time. Schedule with https://tweetdeck.twitter.com/.
4. Follow and be followed back. But do not overdo it. Unfollow who unfollows you https://who.unfollowed.me/.
5. Be aware of the Matthew effect.

→ Be careful with your time! Consider the opportunity cost.

Time to start creating

• our Oxford Social Policy ReproducibiliTea,
• your academic websites,
• our Twitter Community!

PhD Toolkit on Transparent, Open, Reproducible Research

Collections by

• Mark Fransham
• Alex Albright
• Maximilian Kasy
• …