• Office hours:
  • Dr. Çetinkaya-Rundel:
    • Mondays 3:30 - 5:30pm
    • by appointment
  • Nayib: Tuesdays 5-6pm - Wilson 3rd Floor common room
  • Gloria: Wednesdays 5-6pm - Wilson 3rd Floor common room

• Introduction to tools for reproducible data analysis

• In May 2015 Science retracted a study of how canvassers can sway people's opinions about gay marriage published just 5 months ago.

• Science Editor-in-Chief Marcia McNutt: Original survey data not made available for independent reproduction of results. + Survey incentives misrepresented. + Sponsorship statement false.

• Two Berkeley grad students who attempted to replicate the study quickly discovered that the data must have been faked.

• Methods we'll discuss today can't prevent this, but they can make it easier to discover issues.

Source: http://news.sciencemag.org/policy/2015/05/science-retracts-gay-marriage-paper-without-lead-author-s-consent

From the authors of Low Dose Lidocaine for Refractory Seizures in Preterm Neonates:

"The article has been retracted at the request of the authors. After carefully re-examining the data presented in the article, they identified that data of two different hospitals got terribly mixed. The published results cannot be reproduced in accordance with scientific and clinical correctness."

Source: http://retractionwatch.com/2013/02/01/seizure-study-retracted-after-authors-realize-data-got-terribly-mixed/

• The authors informed the journal that the merge of lab results and other survey data used in the paper resulted in an error regarding the identification codes. Results of the analyses were based on the data set in which this error occurred. Further analyses established the results reported in this manuscript and interpretation of the data are not correct.

• Original conclusion: Lower levels of CSF IL-6 were associated with current depression and with future depression […].

• Revised conclusion: Higher levels of CSF IL-6 and IL-8 were associated with current depression […].

Source: http://retractionwatch.com/2014/07/01/bad-spreadsheet-merge-kills-depression-paper-quick-fix-resurrects-it/

• Scriptability \(\rightarrow\) R

• Literate programming \(\rightarrow\) R Markdown

• Version control \(\rightarrow\) Git / GitHub

"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 human beings- what we want a computer to do."

• These ideas have been around for years!
• and tools for putting them to practice have also been around
• but they have never been as accessible as the current tools

• Are the tables and figures reproducible from the code and data?
• Does the code actually do what you think it does?
• In addition to what was done, is it clear why it was done? (e.g., how were parameter settings chosen?)
• Can the code be used for other data?
• Can you extend the code to do other things?

• Go to gort.stat.duke.edu:8787

• Log on with your Net ID and password

• R as a calculator

2 + 2

## [1] 4

factorial(20)

## [1] 2.432902e+18

• Working with variables

x <- 2
x * 3

## [1] 6

• Create a GitHub account at https://github.com/
  • This will be a public account associated with your name
  • Choose a username wisely for future use
  • Don't worry about details, you can fill them in later
• Create a repository called intro_demo
  • Give a brief and informative description
  • Choose "Public"
  • Check the box for "Initialize this repository with a README"
  • Click "Create Repository"

• Go to RStudio

• File -> New Project
  • Version Control: Checkout a project from a version control repository
  • Git: Clone a project from a repository
  • Fill in the info:
    • URL: use HTTPS address
    • Create as a subdirectory of: Browse and create a new folder call sta112

• Note for the future: Each course component you work on (an application exercise, a homework assignment, project, exam, etc.) should be its own repository, and should be fully contained in a folder inside the folder sta112.

• On GitHub (on the web) edit the README document and Commit it with a message describing what you did.

• Then, in RStudio also edit the README document with a different change.
  • Commit your changes
  • Try to push – you'll get an error!
  • Try pulling
  • Resolve the merge conflict and then commit and push

• As you work in teams you will run into merge conflicts, learning how to resolve them properly will be very important.

• Fully reproducible reports

• Simple markdown syntax for text

• Code goes in chunks

Tip: Keep the Markdown cheat sheet handy, we'll refer to it often as the course progresses.

[Live demo – follow along]

Visualize relationship between life expectancy and GDP per capita in 2007 in countries. Also make a plot

Packages are the fundamental units of reproducible R code. They include reusable R functions, the documentation that describes how to use them, and sample data.

• In the following exercises we'll use dplyr (for data wrangling) and ggplot2 (for visualization) packages.

• Load these packages in your markdown file

library(dplyr)
library(ggplot2)

gapminder <- read.csv("https://stat.duke.edu/~mc301/data/gapminder.csv")

• Start with the gapminder dataset

• Filter for cases (rows) where year is equal to 2007

• Save this new subsetted dataset as gap07

gap07 <- gapminder %>%
  filter(year == 2007)

Task: Visualize the relationship between gdpPercap and lifeExp.

qplot(x = gdpPercap, y = lifeExp, data = gap07)

Task: Color the points by continent.

qplot(x = gdpPercap, y = lifeExp, color = continent, data = gap07)

• Stage

• Commit (with a message)

• Push

What if you wanted to now change your analysis

• to subset for 1952

• plot life expectancy (lifeExp) vs. population (pop)

• and size the points by GPD (gpdPercap)
  • hint: add argument size = gpdPercap to your plotting code

Once you're done, commit and push all your changes with a meaningful message.

• Read the following reproducibility case studies:
  • http://news.sciencemag.org/policy/2015/05/science-retracts-gay-marriage-paper-without-lead-author-s-consent
  • http://retractionwatch.com/2013/02/01/seizure-study-retracted-after-authors-realize-data-got-terribly-mixed/
  • http://retractionwatch.com/2014/07/01/bad-spreadsheet-merge-kills-depression-paper-quick-fix-resurrects-it/
• Read the following paper:
  • Hadley Wickham. "Tidy data". Journal of Statistical Software. August 2014, Volume 59, Issue 10. http://www.jstatsoft.org/v59/i10/paper