This repository contains all the code necessary to reproduce the results in the paper "The effect of Behavioral Factors and Intervention Strategies on Pathogen Transmission: Insights from a Two-Week Epidemic Game at Wenzhou-Kean University in China", by Musa et al.
Download the histories.csv file from the following Zenodo repository:
https://zenodo.org/records/10674401
and place it under data. Then you should be able to run the main-epi-analysis.Rmd notebook from RStudio Desktop.
The code was tested with R software version 4.4.1, and it requires the following packages:
- dplyr
- tidyr
- ggplot2
- reshape2
- scales
- patchwork
- cowplot
- lubridate
- zoo
- patchwork
- deSolve
- sfsmisc
The super spreader analysis following the methods from Taube et al. can be run in Jupyter Lab using the super-spreader-analysis.ipynb notebook.
The notebook was tested with python version 3.13.0, and it requires the following packages:
- pandas
- numpy
- scipy
- pickle
- matplotlib
- networkx
- pygraphviz