Dynamic Documents

• Produce content do not focus on “end product”
• Improves clarity
• Reduces errors (potentially)

• Allows for repeatability

  Also it can save you time!
  If done right

• Data
• Code
• Text

• Version Control

  We are going to use:
  RStudio (via Rmarkdown, knitr, and Pandoc)
  Git
  GitHub

  to produce HTML, Word, and .pdf files

R - you should know what this is…
RStudio - an R IDE, text editor, project manager, interface to git
Rmarkdown - language established for creating webpages without all the HTML markup
Pandoc - program to convert one language to another, built into RMarkdown v2
knitr - R package that updates “sweave” and increases flexibility, built into RMarkdown v2
LaTeX - software for typesetting and making .pdf files Git - version control, GitHub - a place for sharing (and backing up) code and files

• Create new repository in github
  
• Create version control RStudio project - linked to github
  
• Work in R/Markdown saving versions with git
  
• Create document/presentation - same general code for both

• Machine & human readable
• How will you share it?
• What happens in the future?

Do NOT make/keep/enable crappy data protocols ever!

• Any data manipulations should be done with code…

• More on data at https://ben-williams.github.io

• Probably the most challenging part to learn
  
• Steep learning curve
  

• Once you learn it you won't go back

  “If you don't use GitHub, use GitHub, end of decision tree - Jim Thorson”

xkcd.com

• Git is used to manage a project, or a set of files, as they change over time.
• Git stores this information in a data structure called a repository.
• A git repository contains:
  • A set of commit objects.
  • A set of references to commit objects, called heads.

• A set of files, reflecting the state of a project at a given point in time.
• References to parent commit objects.
• An SHA1 name, a 40-character string that uniquely identifies the commit object. The name is composed of a hash of relevant aspects of the commit, so identical commits will always have the same name.

• A reference to a commit object.
• Each head has a name.
• By default, there is a head in every repository called master.
• A repository can contain any number of heads.
• At any given time, one head is selected as the “current head”“
  • This head is aliased to HEAD, always in capitals.

• No longer need to save version names.
• Can “go back in time” and checkout older versions.