The site package supports malariaverse users to:
- Access and download the latest country site-files 🌐 ➡️ 💻
- Translate site file information into malariasimulation parameters 🌍 ➡️ 📉
The site-file
The site-file is the file storing all of the sub nationally disaggregated information for a country. Components of the site-file include:
- The metadata, with high level information about the country and site-file version.
- Historical Epidemiological Data with estimates of cases, deaths and parasite prevalence.
- Population and Demography information.
- Estimates of the Historical Intervention Use in the country.
- Rainfalll and Seasonality data.
- Information on the Mosquito Vectors
Accessing and downloading site-files
Please see this detailed guide for information on how to gain access and download site files.
Translating site-file information to malariasimulation parameters
If we have access a site file, then all we need to do to run the model is
- Isolate a single site, this is a single sub-national unit within the country
- Create the parameter list
- Pass that to malariasimulation to run the simulation
# Pull information for a single sub-national unit from the site-file
site <- subset_site(
site = example_site,
site_filter = data.frame(
country = "Burkina Faso",
iso3c = "BFA",
name_1 = "Sahel",
urban_rural = "rural")
)
# Convert site information to malariasimulation parameters
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
)
)
# Run the model!
site_sim <- malariasimulation::run_simulation(
timesteps = site_par$timesteps,
parameters = site_par
)