Link to the published manuscript
This repository includes code used to produce the simulations reported in Herbeck et al.’s “HIV Population-Level Adaptation Can Rapidly Diminish the Impact of a Partially Effective Vaccine”. The source code for EvoNetHIV is contained in the “R” folder, while simulation scripts are stored in “Simulation scripts”. These scripts are written for use with an advanced computational system; as such, we have also provided an example script that users may run on a typical desktop system. To do so, you will need to install the EvoNet package with the following line of code (install devtools first, if not already installed):
devtools::install_github("EvoNetHIV/Herbeck-et-al-Vaccine-2018")
Details of the model are provided in the document “Online technical supplement”.