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This repository contains C++ code and helper R code that can be used to simulate infectious disease dynamics in space. The code takes relative population density and population size as inputs and will create a synthetic population of households that is consistent with both. The natural history of the disease can then be specified in terms of waiting time distributions, based on the natural history of smallpox. Because smallpox has quite a complex natural history, other pathogens such as influenza and Ebola can be mapped onto these. Transmission can occur within the household, across a peer-group network or via purely spatial transmission.
The code has been run under Windows with Visual studio and from the command line under OS X. However, it is now maintained as a linux library, mainly on Ubuntu 18.04 on the Widows subsystem for linux.
It requires:
- gnu C++
- gnu make
- gnu scientific library (developer)
- R statistical package (for the R helper code)