Schedule for session

• Why R?

• What is R Markdown?

• How should we conduct statistical analyses?

  • Data visualization
  • Data manipulation/summarizing
  • Data analysis/modeling
  • Interpretation of results
  • Reproducible research

Why R?

The traditional approach to reports / analysis in the sciences

• Import data set into statistical software package
• Run the procedure to get results
• Copy and paste appropriate pieces from the analysis into document editor
• Add descriptions
• Finish/submit report

Disadvantages of this process

• Lots of manual work (prone to make errors)
• Tedious (who likes to carefully copy-and-paste?)
• Likely not recordable (did you write down all the steps you followed to get your analysis?)
• What if you made an error at the beginning of your analysis? If your data had an error?

What is R?

• R is a completely free software package and language for statistical analysis and graphics.
• It excels in helping you with
  • data manipulation
  • automation
  • reproducibility
  • improved accuracy
  • error finding
  • customizability
  • beautiful visualizations
• Any downsides?

Learning how to use R

RStudio and R Markdown

• RStudio is a powerful user interface that helps you get better control of your analysis.
• It is also completely free.
• It comes in both a desktop version and a server version (on the cloud).
• You can write your entire paper/report (text, code, analysis, graphics, etc.) all in R Markdown.
• If you need to update any of your code, R Markdown will automatically update your plots and output of your analysis and will create an updated PDF/HTML file.
• No more copy-and-paste!

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

## [1] 1000