warmup

library(foresite)

Whilst malariasimulation includes a step to initialise a run as close to equilibrium as possible, it is still necessary to run the model for a burn in period to allow the dynamics to fully equilibrate.

Site files have been run for a burn in period of 10 years pre year 2000, and have been calibrate to data from 2010 onwards. To ensure future runs with site files match, it is important to include this 10 year burn in period. The function site::site_parameters() has an argument burnin to help with this. Any post processing of model runs will likely requier this burn in period to be discarded from, the model output.

Some outputs (e.g. incidence) are more sensitive than others (e.g. prevalence) to the burn in period duration. Ideally a period of 40+ years would be implemented, although this may be computationally challenging.