README.txt

Visualizing Results from Infection Transmission Models: A Case Against
'Confidence Intervals'

Author: Eric Lofgren, MSPH (Eric.Lofgren@unc.edu) 
Affiliation: Dept. of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC

This repository contains electronic supplemental material for the above
named article. This includes the following files:

visualizing_code.r: The R code necessary to reproduce the analysis and
data visualization featured in the manuscript.

Visualizing_data.csv: A comma-separated dataset of the epidemic
simulation used as a worked data visualization example in the
manuscript. This file is necessary to run the included R code, and to
exactly replicate the results of the stochastic epidemic simulation.

eFigure1.pdf: A supplemental figure combining several methods of
visualization to both show the full scope of simulation results and
highlight specific trajectories of interest.

Instructions for Use:
Click on 'visualizing_data.dat' on the main list of files. Right click 'Raw' and save the file to your hard drive. Navigate back to the main page and click on 'visualizing_code.r'. Follow the same procedure to download the R code, or click 'Raw' to see the code to cut-and-paste directly into your R console. Change your R working directory to the directory where you downloaded the data file and run the supplied R code. Figures will be output as a series of .pdf files.