Helper Scripts

Helper Scripts

There are many common tasks/analyses any user will likely wish to perform on simulated datasets generated by FAVITES. To assist users, we have created a series of "helper scripts" that perform various to perform tasks we thought would be typical of many simulation experiments. These helper scripts can be found in the helper_scripts directory of the FAVITES repository.

Network Visualization

FAVITES outputs the transmission network in the FAVITES format, which was designed to be easy to parse using basic Unix commands, but the GEXF format is a network format that is commonly used by popular network tools. We have included a helper script, FAVITES2GEXF.py, to convert from the FAVITES format to the GEXF format. To visualize the transmission network, we recommend opening the GEXF transmission network in Gephi, a popular cross-platform open-source tool. The GEXF transmission network FAVITES2GEXF.py outputs is a dynamic network, meaning you can use Gephi to visualize the growth of the transmission network over time.

In the GEXF file, each node is given a single attribute, "infected," which is set to false at time 0 and is set to true upon infection, and each edge is given a single attribute, "transmission," which is set to false at time 0 and is set to true upon a transmission event along that edge. Simply load the GEXF file outputted by FAVITES in Gephi, go to the "Appearance" box, go to the "Nodes" tab to set the desired colors for infected and uninfected (which would be "true" and "false" for the "infected" attribute, respectively), go to the "Edges" tab to set the desired colors for transmission edges and normal contact network edges (which would be "true" and "false" for the "transmission" attribute, respectively), and set "Enable auto transformation - applied continuously" to have the colors change automatically in the timeline view.