CSDNoise

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

CSDNoise

Getting Started

Installing dependencies

To (locally) reproduce this project, do the following:

0. Download this code base. You can do this by cloning the repository or by downloading the zip file. Notice that raw data are not included in the git-history and may need to be downloaded independently.

1. Install Julia. I would recommend you use the juliaup installer as it makes it much easier to deal with multiple versions of Julia, as well as keep them up to date.

2. Open a Julia console and do:

   julia> using Pkg
   julia> Pkg.add("DrWatson") # install globally, for using `quickactivate`
   julia> using DrWatson
   julia> @quickactivate "CSDNoise"
   julia> Pkg.instantiate()
   

This will install all necessary packages for you to be able to run the scripts and everything should work out of the box, including correctly finding local paths.

You may notice that most scripts start with the commands:

using DrWatson
@quickactivate "CSDNoise"

which auto-activate the project and enable local path handling from DrWatson.

Running the project

To run the project, you can use the Justfile. First, you should make sure you have both Just and Typst installed on your computer. You can do so by following the instructions at the Just manual and Typst's GitHub Page for the CLI.

Once you have a version of Just and Typst installed you can use the following terminal command to run the Justfile:

just manuscript

Project Structure

❯ tree -L 2
.
├── Justfile
├── Manifest.toml
├── manuscript
│   ├── combined-manuscript.pdf
│   ├── combined-manuscript.typ
│   ├── CSD.bib
│   ├── manuscript_files
│   ├── manuscript.pdf
│   ├── manuscript.typ
│   ├── scripts
│   │   ├── optimal-thresholds.jl
│   │   └── plotting-setup.jl
│   ├── supplemental_files
│   ├── supplemental-appendix.pdf
│   ├── supplemental-appendix.typ
│   └── template.typ
├── out
│   └── ensemble
│       ├── ews-hyperparam-optimization
│       └── seasonal-infectivity-import
├── plots
├── Project.toml
├── README.md
├── scripts
│   ├── calculate-dynamical-noise-vaccintion-rates.jl
│   ├── ensemble-sim_ews-optimization.jl
│   ├── ensemble-sim_ews-optimization.log.txt
│   ├── ensemble-sim_ews-visualization.jl
│   ├── ensemble-sim_ews-visualization.log.txt
│   ├── ensemble-sim_inferred-scenario-visualizations.jl
│   └── ensemble-sim.jl
├── src
│   ├── ARCHIVE
│   ├── cairomakie-plotting-setup.jl
│   ├── CSDNoise.jl
│   ├── detection-thresholds.jl
│   ├── diag-testing-functions.jl
│   ├── dynamics-constants.jl
│   ├── ensemble-functions.jl
│   ├── ensemble-sim_single-scenario_plots.jl
│   ├── ews-functions.jl
│   ├── ews-hyperparam-optimization.jl
│   ├── ews-metrics.jl
│   ├── ews-survival.jl
│   ├── helpers.jl
│   ├── makie-plotting-setup.jl
│   ├── noise-functions.jl
│   ├── plotting-functions
│   ├── SEIR-model.jl
│   ├── structs.jl
│   ├── test-constants.jl
│   └── transmission-functions.jl
├── test
│   ├── ews-functions.jl
│   ├── ews-metrics.jl
│   └── runtests.jl
└── workflows
    └── CI.yml

25 directories, 86 files

• out/ensemble
  • ews-hyperparam-optimization contains the *.jld2 files that save the results of the optimizations.
  • seasonal-infectivity-import contains the *.jld2 files that save the results of the SEIR simulations.
• plots contains all output plots from temporary scripts.
• scripts contains the Julia scripts used to examine single and ensemble simulations, using plotting and other functions defined in src/*.jl files.
• src contains all Julia source files and functions used in the analysis pipeline and exploration scripts. These files are separated by purpose.
• manuscript contains all files relevant to the manuscript.
  • combined-manuscript.typ is an outer file that includes both the manuscript.typ and supplemental-appendix.typ files for cross-referencing.
  • scripts/optimal-thresholds.jl contains all function calls to generate the underlying simulation results and figures and tables for the manuscript.
• test contains all test scripts.
• workflows contains the CI workflow using GitHub Actions. Currently it only contains a file that can run tests on push to the main branch, but it is not active.