Why this template was needed

“Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them.”

• Roger Peng, Johns Hopkins

Why would reproducible research be
of value with senior theses?

• Updating your code at the very beginning has little impact on all of your analysis throughout the rest of the document
• Helps you remember how you performed your analysis YEARS down the road
• Gets you prepared for submitting journal articles that may require revisions
• Assists in others building off/from your work
• Companies are moving more and more towards reproducible research/analysis to help with employee turnover/documentation

What is Markdown?

• A “plaintext formatting syntax”
• Type in plain text, render to more complex formats
• One step beyond writing a txt file
• Render to HTML, PDF, etc.

What does it look like?

  # Header 1
  
  ## Header 2
  
  Normal paragraphs of text go here.
  
  **I'm bold**
  
  [links!](http://rstudio.com)
  
   * Unordered
   * Lists   
   
  And  Tables
  ---- -------
  Like This
  

What is R Markdown?

• “Literate programming”
• Embed R code in a Markdown document
• Renders textual output along with graphics

```{r}
x <- rnorm(1000)
length(x)
qplot(x, bins = 10, 
      fill = I("orange"), 
      color = I("black"))
```

## [1] 1000

The Reed College
R Markdown
Senior Thesis Template

Demo of getting
the template
up-and-running

(Following along with blog here)

Resources

Markdown Cheatsheet

R Markdown Reference Guide

My reedtemplates package

Thanks!

cismay@reed.edu

• Blogpost about this thesis template
• Code for slide creation on my GitHub page
• Slides available here