1. Introductions
2. Class overview
3. Getting R up and running

Investigator, Lieber Institute for Brain Development Assistant Professor, Department of Mental Health, JHSPH

PhD in Epidemiology, MHS in Bioinformatics

Email: ajaffe@jhu.edu

Leonardo Collado-Torres

5th year PhD student in Biostatistics

Email: lcollado@jhu.edu

Shaun Truelove

4th year PhD student in Epidemiology

Email: struelo1@jhu.edu

What do you hope to get out of the class?

Why R?

http://www.aejaffe.com/summerR_2015/

Materials will be uploaded the night before class

• Reading data into R
• Recoding and manipulating data
• Writing R functions and using add-on packages
• Making exploratory plots
• Understanding basic programming syntax
• Performing basic statistical tests

• 3 modules per class session, each approximately 1 hour
  • "Interactive" Lecture with RStudio + slides
  • Lab/Practical experience

1. Attendance/Participation: 20%
2. Nightly Homework: 3 x 15%
3. Final "Project": 35%

• Homework 1: Due Tuesday 6/16 by 5pm

• Homework 2: Due Wednesday 6/17 by class

• Homework 3: Due Thursday 6/18 by class

• Project: Due Friday 7/3 by 5pm

• R is a language and environment for statistical computing and graphics

• R is the open source implementation of the S language, which was developed by Bell laboratories

• R is both open source and open development

(source: http://www.r-project.org/)

• Powerful and flexible

• Free (open source)

• Extensive add-on software (packages)

• Designed for statistical computing

• High level language

• Fairly steep learning curve

  • "Programming" oriented

  • Minimal interface

• Little centralized support, relies on online community and package developers

• Annoying to update

• Slower, and more memory intensive, than the more traditional programming languages (C, Java, Perl, Python)

Install the latest version from: http://cran.r-project.org/

If you have an older version of R, you may not need to update. If you do want to update, re-install and run

update.packages(ask=FALSE)

(Makes R easier)

• Integrated Development Environment (IDE) for R
  • Syntax highlighting, code completion, and smart indentation
  • Execute R code directly from the source editor
  • Easily manage multiple working directories using projects
  • Workspace browser and data viewer
  • Plot history, zooming, and flexible image and PDF export
  • Integrated R help and documentation
  • Searchable command history
• http://www.rstudio.com/

• The R Console "interprets" whatever you type
  • Calculator
  • Creating variables
  • Applying functions
• "Analysis" Script + Interactive Exploration
  • Static copy of what you did (reproducability)
  • Try things out interactively, then add to your script
• R revolves around functions
  • Commands that take input, performs computations, and returns results
  • Many come with R, but people write external functions you can download and use

• Ctrl + Enter (Cmd + Enter on OS X) in your script evaluates that line of code
  • It's like copying and pasting the code into the console for it to run.
• Ctrl+1 takes you to the script page
• Ctrl+2 takes you to the console
• http://www.rstudio.com/ide/docs/using/keyboard_shortcuts

• Homework will involve working through: http://tryr.codeschool.com/
• UCLA Institute for Digital Research and Education: http://www.ats.ucla.edu/stat/r/
• R reference card: http://cran.r-project.org/doc/contrib/Short-refcard.pdf
• Undergrad Guide to R: https://sites.google.com/site/undergraduateguidetor/
• Quick R: http://statmethods.net/