knitr and markdown EPID 799C Fall 2017 To get ready for today: Create new  markdown file (word or html) If it doesn’t work, follow the package prompts…

Why? The loop for generating papers in specific and knowledge in general takes too long to re/iterate. Integrating analysis and outputs / formatting is a key obstacle to that loop. What if you could push a button and rebuild your paper / website / presentation from scratch?

A manifesto for reproducible science https://www.nature.com/articles/s41562-016-0021

rOpenSci Our Vision and Mission rOpenSci fosters a culture that values open and reproducible research using shared data and reusable software. We do this by:  Creating technical infrastructure in the form of carefully vetted, staff- and community-contributed R software tools that lower barriers to working with scientific data sources on the web Creating social infrastructure through a welcoming and diverse community Making the right data, tools and best practices more discoverable building capacity of software users and developers and fostering a sense of pride in their work Building capacity of software users and developers and fostering a sense of pride in their work Promoting advocacy for a culture of data sharing and reusable software. https://ropensci.org/about/

What is Markup? Specific Markup language: HTML = Hypertext Markup Language

Why Markdown? Markdown produces Markup Abstracted to minimize coding Can be sent to multiple platform-specific markup outputs (word, html, etc.)

What is R Markdown? From the cheat sheet…

Let’s Try!