Corona.jl

Corona.jl performs the assimilation of epidemiological data using an augmented SIR model.

Getting started

You can get started with Corona.jl in a few steps:

1. Install Corona.jl
2. Install the dependecies
3. Prepare data
4. Run the data assimilation
5. Analyze the results

Installing Corona.jl

1. Clone Corona.jl (replace /path/to/julia/modules with your desired path):

git clone https://github.com/sesterhenn/Corona.jl /path/to/julia/modules/Corona

2. Add to ~/.julia/config/startup.jl the following line (unless /path/to/julia/modules is already added to your Julia LOAD_PATH variable):

push!(LOAD_PATH,"/path/to/julia/modules/Corona")

where "/path/to/julia/modules/Corona" is the folder containing Corona.jl

Installing dependencies

Execute

  ] add Dates TimeSeries DataStructures DifferentialEquations LinearAlgebra Flux Interpolations FFTW FileIO JLD2 DataFrames Unicode CSV Formatting Plots LaTeXStrings

from the Julia REPL.

Preparing data

1. Provide your preferred data paths in config/paths.jl as shown in config/example-paths.jl.
2. Provide information on the data sources in config/data.jl following the structure of config/example-data.jl.

For a quick start, you can use the fake data in the files raw/native/example-Laputa.csv and raw/example-population.csv, by copying them to raw/native/Laputa.csv and raw/population.csv, respectively.

Running the data assimilation

Move to the installation folder, modify the Julia script script/run_DA.jl as desired and execute

  include("script/run_DA.jl")

from the Julia REPL.

Analyzing the results

Move to the installation folder (if you are not already there), modify the Julia script script/analyze_DA.jl as desired and execute

  include("script/analyze_DA.jl")

from the Julia REPL.

License

This package is free to use for noncommercial purposes and for commercial purposes during a trial period under the terms of the Prosperity Public License.