Reproducibility and automation

Makefiles

“Automation with make”, Section 5.1 of Kieran Healy, The Plain Person’s Guide to Plain Text Social Science
Karl Broman, “Minimal make: A minimal tutorial on make”
Introduction to make

How to install make:

macOS:
1. Run xcode-select --install
Windows:
1. Install chocolately
2. Run choco install make

Sample Makefile

(Important! You must use tabs in Makefiles, not spaces)

# Read as "mypaper.pdf depends on mypaper.md and figures/fig1.jpg"
mypaper.pdf: mypaper.md figures/fig1.jpg
  pandoc mypaper.md --citeproc -o mypaper.pdf

# Read as "figures/fig1.jpg depends on analysis/figs.R"
figures/fig1.jpg: analysis/figs.R 
  Rscript analysis/fig.R

Reproducible research

Justin Kitzes, Daniel Turek, and Fatma Deniz, The Practice of Reproducible Research: Case Studies and LEssons from the Data-Intensive Sciences
Karl Broman, “Initial steps toward reproducible research”
Ben Marwick, “rrtools: Tools for Writing Reproducible Research in R”
Anna Krystalli, "Creating a research compendium w/ rrtools