dc9 - 0.5

DebConf9

Speakers
Don Armstrong
Schedule
Day DebConf day 5 / Conference dinner (2009-07-28)
Room BOF room - no video
Start time 19:00
Duration 01:00
Info
ID 435
Event type workshop
Track DebConf Unofficial
Language en
Feedback

Reproducible Research with R and Sweave

My life outside of Debian

My glamorous day (and often, night) job is working on finding the genes which cause Systemic Lupus Erythematosus (SLE) and in a separate project, determining how arteriovenous malformations (AVM) in the brain occur. Being able to reproduce the research that I've conducted in the past is of critical importance, especially when dealing with millions of datapoints in projects spread over years.

The utilization of tools such as R and Sweave, which enable the production of publication-quality plots, tables, and even text in articles that are tied to the raw data (using make), allows researches such as myself to be able to replicate an analysis in the future, and know precisely where we've found mistakes. In this talk, the basics of R and Sweave will be presented, as well as a set of examples, ranging from simple to relatively complex.

  • Basics of R
    • basic datatypes (lists, vectors, matrices)
    • basic operations
    • basic functions
    • basic plotting
      • devices
      • time
    • basic modeling
  • Basics of Sweave
    • embedding R in LaTeX
    • tricks for keeping everything in sync
  • Examples
    • Regenerating the RC bug graph
    • Examining expression differences in AVM
    • Genes associated with SLE