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Daedalus.jl

License:MIT Version Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept. Dev Build Status Coverage SciML Code Style

Daedalus.jl is a Julia package that aims to mirror the R package {daedalus}.

Daedalus.jl is developed at the Jameel Institute at Imperial College London as part of the Jameel Institute-Kenneth C. Griffin Initiative for the Economics of Pandemic Preparedness (EPPI), in collaboration with the RESIDE research software engineering team.

Note that functionality compared to the R package is still limited.

Installation

Daedalus.jl can be installed from GitHub using the Julia package manager Pkg.jl.

using Pkg
Pkg.add(url="git@github.com:jameel-institute/Daedalus.jl.git")

Quick start

using Daedalus
using Plots

# pump up r0 to get peak within 50 days
infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
data = daedalus("Canada", infection, time_end=600.0);

# plot exposed group
times = Daedalus.Outputs.get_times(data)
# functioning get_values() bins into 90 days by default, set to 1 for no binning
exposed = Daedalus.Outputs.get_values(data, "E", 1)
hosp = Daedalus.Outputs.get_values(data, "H", 1)

# plot the output to see lag in hospitalisations
plot(times, exposed, label="exposed")
plot!(times, hosp, label="hosp")
xlabel!("Time (days)")
ylabel!("# individuals")
Example block output
# plot recorded Rt
vecRt = Daedalus.Outputs.get_values(data, "Rt", 1)
plot(times, vecRt, label="Rt")
xlabel!("Time (days)")
ylabel!("Rt")
Example block output
  • The Daedalus integrated epi-econ model provided by the R package daedalus.

Help

To report a bug, request a feature, or just start a discussion, please open an issue.