CovidReproductionNumber.jl

Install dependencies

You need julia installed, preferably a version higher than 1.6.

You can run Julia in the directory of CovidReproductionNumber.jl, using the project environment as:

cd CovidReproductionNumber.jl
julia --project=.

After that, type

Pkg.instantiate()

This should install the necessary Julia packages.

Run the R estimators

We assume your input is placed in input/data-20220103.xlsx. The input excel file must contain a single sheet with several correctly marked columns. You can check the suitability of the input file using script check_input.jl, as follows:

julia --project=. check_input.jl input/data-20220103.xlsx

You may get an output like this (or eventually an error with a description of the problem):

┌ Warning: Last entry is older than 1 week!
└ @ Main ~/work/CovidReproductionNumber.jl/check_input.jl:36
[ Info: Age of the last entry is 136 days
[ Info: Check finished OK.

Reff and Rt analyses may be run as follows:

julia --project=. estimate_r_eff.jl input/data-20220103.xlsx
julia --project=. estimate_r_t.jl input/data-20220103.xlsx

The output should be generated into corresponding files:

input/Reff_estimate_data-20220103.xlsx.csv
input/Rt_estimate_data-20220103.xlsx.csv