site

Site acts as a translational layer between a site file and malariasimulation: 🌍 ➡️ 📉

The site file is the file storing all of the context specific information for a site, such as historical intervention coverage, seasonality, vectors etc. To simulate a given site, we must convert this information into an input parameter list for malaria simulation. That is what site is here to do!

If we have a correctly configured site file example_site, then all we need to do is create the parameter list and pass that to malariasimulation to run:

site <- subset_site(example_site, example_site$eir[1,])
site_par <- site_parameters(
  interventions = site$interventions,
  demography = site$demography,
  vectors = site$vectors$vector_species,
  seasonality = site$seasonality$seasonality_parameters,
  eir = site$eir$eir,
  overrides = list(
    human_population = 1000
  )
)
site_sim <- malariasimulation::run_simulation(
  timesteps = site_par$timesteps,
  parameters = site_par
)

Installation

You can install the development version of site from GitHub with:

# install.packages("devtools")
devtools::install_github("mrc-ide/site")