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Dynamic_Documents.Rpres
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Dynamic Documents
========================================================
author: Ben Williams
date: October 20 & 22, 2015
What are 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*
What is needed:
=======================================================
- 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
Tools
========================================================
**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
Basic workflow
========================================================
- 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
Data
========================================================
- 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
Git & GitHub
========================================================
- 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"
Why Git Rules
========================================================
Why might Git not rule?
==================================
*xkcd.com*
How Git works
========================================================
- 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 Commit contains
========================================================
- 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 Head contains
========================================================
- 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.
Why Git is great
=======================================================
- No longer need to save version names.
- Can "go back in time" and checkout older versions.
How Rmarkdown works
=======================================================
