safir: squire and friends individual rewrite (and maintains the squire naming theme). It uses the {individual} package to specify and run the simulation.

safir can run individual based stochastic versions of the squire and nimue models, which recover trajectories from those aggregated population models (see package vignettes). It also implements a model for vaccination with an arbitrary number of doses and antibody titre dynamics which affect protective efficacy as well as efficacy against severe disease outcomes.

Because safir implements multiple models as individual based simulations, there is a large amount of code, but the central disease progression is shared across the models within safir. Each vignette describes how the simulation functions and where the relevant code can be found.

Installation

install_github('mrc-ide/safir')
library(safir)

Documentation

{safir} is documented on a dedicated website.

This includes the following vignettes:

• Squire Validation Run: comparison of {safir} to {squire}.
• Nimue Validation Run: comparison of {safir} to {nimue}.
• Vaccine model with multiple doses: runs the model for explicit tracking of antibody titre for a 2 dose vaccine.
• Natural Immunity: demonstrates how to modify the vaccine model to also include mechanistic incorporation of natural immunity from infection, as opposed to a generic R (recovered) class.
• Modeling of antibody titre and immunity: describes how antibody titre and protection against infection and severe disease is modeled.
• Differential modeling of infection and vaccine derived NATs: is a short description of how to model differential boost/decay of vaccine and infection derived neutralizing antibody titres.