country_data.md

CurrentModule = Daedalus

Country and pathogen data

Daedalus.jl bundles demographic, economic, and epidemiological data that mirrors the R package {daedalus.data}. All data access is provided through the DataLoader sub-module, which lazy-loads CSV files on first access and caches results for subsequent calls.

Listing available data

using Daedalus

# All countries with bundled demographic + economic data
countries = Daedalus.DataLoader.list_countries()
println("$(length(countries)) countries available")
println("First five: ", countries[1:5])

# All seven reference pathogens
Daedalus.DataLoader.list_pathogens()

# Pandemic response (economic closure) strategies
Daedalus.DataLoader.list_closure_strategies()

# Pre-pandemic vaccine investment scenarios
Daedalus.DataLoader.list_vaccination_scenarios()

Country data

DataLoader.get_country returns a DataLoader.CountryData struct containing demography, a 4×4 social contact matrix, sector workforce counts, gross value added (GVA) per sector, and hospital capacity.

using Daedalus

uk = Daedalus.DataLoader.get_country("United Kingdom")

println("Demography (4 age groups): ", uk.demography)
println("Hospital capacity (spare beds): ", uk.hospital_capacity)
println("Number of economic sectors: ", length(uk.workers))

# 4×4 social contact matrix
uk.contact_matrix

Pathogen data

DataLoader.get_pathogen returns an DataLoader.InfectionData struct with all epidemiological parameters derived from the seven reference pathogens.

using Daedalus

delta = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")

delta

Preparing country inputs for the model

Pass a country name string and a pathogen name to daedalus to run the model with country-specific demography, contacts, and workforce data:

using Daedalus

result = daedalus("United Kingdom", "sars-cov-2 delta", time_end=600.0)

You can also pass a DataLoader.CountryData struct directly and customize infection parameters. This is useful when you want to pre-fetch or modify country or infection data before running the model:

# Pre-fetch country data and pass the struct directly
uk = Daedalus.DataLoader.get_country("United Kingdom")
infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
infection.r0 = 2.5
result2 = daedalus(uk, infection, time_end=600.0)

The Data sub-module also exposes lower-level functions for inspecting or manipulating the country arrays directly. Each function accepts either a country name String or a CountryData struct:

Function	Returns
initial_state(country)	Initial epidemic state array (N_GROUPS × N_COMPARTMENTS × N_VAX_STRATA)
prepare_contacts(country)	Scaled 49×49 contact matrix
worker_contacts(country)	Per-capita within-sector contact rates (length-45 vector)
prepare_demog(country)	49-element population vector

Running Daedalus with country and infection structs

Pass a country name string directly to daedalus to use country-specific demography, contact patterns, and workforce data.

using Daedalus
using Plots

# Run the model using UK demography and contact patterns
infection_uk = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
infection_uk.r0 = 2.5
data_uk = daedalus("United Kingdom", infection_uk, time_end=600.0)

times_uk = Daedalus.Outputs.get_times(data_uk)
exposed_uk = Daedalus.Outputs.get_values(data_uk, "E", 1)
hosp_uk = Daedalus.Outputs.get_values(data_uk, "H", 1)

plot(times_uk, exposed_uk, label = "exposed")
plot!(times_uk, hosp_uk, label = "hospitalised")
xlabel!("Time (days)")
ylabel!("# individuals")
title!("United Kingdom — SEIR dynamics")

# Effective reproduction number over time
rt_uk = Daedalus.Outputs.get_values(data_uk, "Rt", 1)
plot(times_uk, rt_uk, label = "Rt", color = :red)
hline!([1.0], linestyle = :dash, color = :black, label = "Rt = 1")
xlabel!("Time (days)")
ylabel!("Rt")
title!("United Kingdom — effective reproduction number")

See Country and pathogen data for a full overview of the bundled data and how to use pathogen-specific parameters.