Reproducible Research


Fall 2015 - Data @ Reed Research Skills Workshop Series

Chester Ismay

Office: ETC 223

cismay@reed.edu

http://blogs.reed.edu/datablog

Who am I?

  • Grew up in South Dakota (town of 112 people)
  • BS in Math, minor in Computer Science from SDSM&T
  • MS in Statistics from Northern Arizona University
  • Worked as an actuary before obtaining PhD in Statistics from Arizona State University
  • Was Assistant Professor of Statistics and Data Science at Ripon College the last two years
  • Moved to Portland area this summer
  • Started working at Reed on August 11th

What can I help you with?

  • Data analysis
  • Data wrangling/cleaning
  • Data visualization
  • Data tidying/manipulating
  • Reproducible research

When am I available?

  • Email me at cismay@reed.edu or chester.ismay@reed.edu
  • Office (ETC 223) hours
    • Mondays (11 AM to noon)
    • Tuesdays and Thursdays (2 PM to 3 PM)
  • Sometimes available for virtual office hours via Google Hangouts (email me for details)

Basic research process

Research Process

Further support

data@reed.edu
http://www.reed.edu/data-at-reed

Research Process

Traditional approaches to writing a statistical report

The dreaded copy-and-paste

  • 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?

Reproducible research

“Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to humans what we want the computer to do.”

  • Donald Knuth, Literate Programming (1984)

“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

R Studio
+
R Markdown

Tools to make working with R friendly

  • RStudio is a powerful user interface that helps you get better control of your analysis.
  • Like R, it is also completely free.
  • 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 file.
  • No more copy-and-paste!
  • It’s my job!

R Markdown

R Markdown

Demonstration on using R Markdown

Garrett Grolemund’s Demo

Chunk options

Option Result
echo = FALSE Don’t include the code
results = "hide" Don’t include the output
include = FALSE Don’t show code or output
eval = FALSE Don’t evaluate the code at all
warning = FALSE Don’t show R warnings
message = FALSE Don’t show R messages
fig.width = # Width of figure
fig.height = # Height of figure

Parameterized reports

Right click on the link to the .Rmd file here, save it, and open it in RStudio.

The Reed R Markdown Thesis Template

(Preliminary edition)

Run this code

if(!require(devtools))
  install.packages("devtools")
if (!require(rticles)){
  library(devtools)
  devtools::install_github("ismayc/rticles")
  }

R Markdown Template

Markdown Cheatsheet

R Markdown Reference Guide

Parameterized Reports Tutorial

My rticles package

Thanks!

cismay@reed.edu



Slides available at http://rpubs.com/cismay/rr_workshop_2015