This folder contains R notebooks and scripts to calculate the MLE of the parameters of the mumps epidemic models for Harvard University and Ohio State University.
The .Rmd notebooks can be run from within RStudio, using the desired properties files. Otherwise, the .R scripts for Harvard and OSU can be run from the command line as follows:
./run_harvard fast.properties
./run_ohio fast.properties
The results from these scripts are presented in the following pre-print:
https://www.medrxiv.org/content/10.1101/2020.07.31.20166348v2
Note: The calculations use the "opt" parameter set, so the reported point estimates of the epidemiological parameters correspond to the maximum of the log-likelihood function.