This repository contains a reproduction of the analysis code for "Dynamics of persistent oral cytomegalovirus shedding during primary infection in Ugandan infants." The article has been published in the Journal of Infectious Diseases: http://jid.oxfordjournals.org/content/214/11/1735
A copy of the Supplement is also located here.
The main components of the analysis are:
#1) All of the data used in the analysis
#2) General Episode Analysis
#3) Mathematical Model Analysis
Figures and tables included in the manuscript were generated from this code. Model fitting was done using a cluster server. The code used for that analysis is in this repo but only for reference. R version and package version information (including the info from the server) is available in the R-version-info directory.
citation:
Mayer BT, Matrajt L, Krantz E, Corey L, Casper C, Gantt S, Schiffer JT. “Dynamics of persistent oral cytomegalovirus shedding during primary infection in Ugandan infants.” Journal of Infectious Diseases. 214(11): 1735-1743. 2016. PMID: 27651417, PMCID: PMC5144733.DOI: 10.1093/infdis/jiw442